From 0aa4f01e55c1df58bfea032231bab0d13c1c7d90 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Wed, 31 Aug 2022 22:25:37 +0200 Subject: [PATCH 1/7] add new pipeline --- CMakeLists.txt | 49 + src/ChrCopyNumber.cpp | 401 ++ src/ChrCopyNumber.h | 49 +- src/GenomeCopyNumber.cpp | 3797 ++++++++++-------- src/GenomeCopyNumber.h | 47 +- src/GenomeGMM.cpp | 463 +++ src/GenomeGMM.h | 87 + src/Makefile.freec | 8 +- src/MixtureComponent.cpp | 142 + src/MixtureComponent.h | 50 + src/SVfinder.h | 2 +- src/ThreadPool.h | 13 +- src/bayes_opt.cpp | 261 ++ src/bayes_opt.h | 35 + src/cumNormalDistr.cpp | 65 + src/cumNormalDistr.h | 14 + src/depend.mk | 8104 ++++++++++++++++++++++++++++++++++++++ src/gaussianKernel.cpp | 68 + src/gaussianKernel.h | 23 + src/main.cpp | 108 +- src/myFunc.cpp | 107 +- src/myFunc.h | 14 +- 22 files changed, 12150 insertions(+), 1757 deletions(-) create mode 100644 CMakeLists.txt create mode 100644 src/GenomeGMM.cpp create mode 100644 src/GenomeGMM.h create mode 100644 src/MixtureComponent.cpp create mode 100644 src/MixtureComponent.h create mode 100644 src/bayes_opt.cpp create mode 100644 src/bayes_opt.h create mode 100644 src/cumNormalDistr.cpp create mode 100644 src/cumNormalDistr.h create mode 100644 src/depend.mk create mode 100644 src/gaussianKernel.cpp create mode 100644 src/gaussianKernel.h diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..6cacbdb --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,49 @@ +cmake_minimum_required(VERSION 3.21) +project(ploidy-purity-cpp) + +if(NOT CMAKE_BUILD_TYPE) +set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "" FORCE) + +set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O0") +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0") + +endif(NOT CMAKE_BUILD_TYPE) +SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic") +SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3") +option(test "Build tests." ON) + +find_package(NLopt) +add_definitions(-DUSE_NLOPT) +add_definitions(-DPROFILE_TRACE) +add_definitions(-DCLUSTER) + +file(GLOB ppc_src + "src/*.h" + "src/*.cpp" + ) + +find_package (Eigen3 3.3 REQUIRED NO_MODULE) +add_executable(PPC src/main.cpp ${ppc_src}) + +target_include_directories(PPC PUBLIC limbo/src) +target_link_libraries(PPC Eigen3::Eigen) + +get_cmake_property(_variableNames VARIABLES) +list (SORT _variableNames) +foreach (_variableName ${_variableNames}) + message(STATUS "${_variableName}=${${_variableName}}") +endforeach() + +find_package(OpenMP) +if (OPENMP_FOUND) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") +endif() + +find_package(Boost 1.74.0 COMPONENTS date_time filesystem system) +include_directories(${Boost_INCLUDE_DIRS}) +target_link_libraries(PPC Eigen3::Eigen ${Boost_LIBRARIES}) +target_include_directories(PPC PUBLIC ${NLOPT_INCLUDE_DIRS}) +target_link_libraries(PPC ${NLOPT_LIBRARIES}) diff --git a/src/ChrCopyNumber.cpp b/src/ChrCopyNumber.cpp index b9d01c8..a8d317a 100644 --- a/src/ChrCopyNumber.cpp +++ b/src/ChrCopyNumber.cpp @@ -20,6 +20,9 @@ A copy of the GNU General Public License is available at #include "ChrCopyNumber.h" +#include +#include +#include using namespace std ; @@ -1773,3 +1776,401 @@ void* ChrCopyNumber_calculateBAFBreakpoint_wrapper(void *arg) } return NULL; } + + +// Added by Gara +/* +void ChrCopyNumber::sampleBAFinWindow() +{ + for (unsigned int i = 0; i < BAFvalues_.size(); i++) { + std::random_device r; + std::string baf = BAFvalues_[i]; + if (baf == "") { + BAF_in_window_.push_back(-1); + } else { + if (baf.find(';') == std::string::npos) { + BAF_in_window_.push_back(std::stof(baf)); + } else { + std::vector bafs_in_window; + std::string segment; + std::stringstream bafs; + bafs << baf; + while(std::getline(bafs, segment, ';')) { + bafs_in_window.push_back(std::stof(segment)); + } + std::default_random_engine e1(r()); + std::uniform_int_distribution<> unif(1, bafs_in_window.size()); + BAF_in_window_.push_back(bafs_in_window[(unif(e1)-1)]); + } + } + } +} +*/ + +/* +void ChrCopyNumber::createRatioAndBAFFromSNPs(SNPinGenome& snpingenome) +{ + std::cout << "Chromosome: " << chromosome_ << std::endl; + int start = 0; + int end = 0; + for (unsigned int i = 0; i < BAFvalues_.size(); i++) { + std::string baf = BAFvalues_[i]; + if (baf == "") { + // do nothing + } else { + float r = ratio_[i]; + float m = medianProfile_[i]; + if (r != -1) { + if (baf.find(';') == std::string::npos) { + BAF_per_SNPs_.push_back(std::stof(baf)); + ratio_per_SNPs_.push_back(r); + median_ratio_per_SNPs_.push_back(m); + + // Calculate fragment length + if (median_ratio_per_SNPs_.size() >= 2) { + if (median_ratio_per_SNPs_.rbegin()[0] != median_ratio_per_SNPs_.rbegin()[1]) { + end = median_ratio_per_SNPs_.size() - 1; + int frag_length = end - start; + fragment_lengths_per_snps_pos_.push_back(frag_length); + start = end; + } + } + } else { + std::vector bafs_in_window; + std::string segment; + std::stringstream bafs; + bafs << baf; + while(std::getline(bafs, segment, ';')) { + bafs_in_window.push_back(std::stof(segment)); + } + for (int j = 0; j < bafs_in_window.size(); j++) { + BAF_per_SNPs_.push_back(bafs_in_window[j]); + ratio_per_SNPs_.push_back(r); + median_ratio_per_SNPs_.push_back(m); + } + // Calculate fragment length + int j = bafs_in_window.size() - 1; + if (median_ratio_per_SNPs_.size() > (j+1)) { + if (median_ratio_per_SNPs_.rbegin()[0] != median_ratio_per_SNPs_.rbegin()[j+1]) { + end = median_ratio_per_SNPs_.size() - j - 1; + int frag_length = end - start; + fragment_lengths_per_snps_pos_.push_back(frag_length); + start = end; + } + } + } + } + } + } + int frag_length = median_ratio_per_SNPs_.size() - start; + fragment_lengths_per_snps_pos_.push_back(frag_length); + + std::cout << "Fragments length: "; + for (int f = 0; f < fragment_lengths_per_snps_pos_.size(); f++) { + std::cout << fragment_lengths_per_snps_pos_[f] << " "; + } + std::cout << std::endl; +} +*/ + + +void ChrCopyNumber::createRatioAndBAFFromSNPs(SNPinGenome& snpingenome) +{ + int index_chr = snpingenome.findIndex(chromosome_); + if (index_chr == NA) { + cerr << "An error occurred in GenomeCopyNumber::printBAF: could not find an SNP index for chromosome " << chromosome_ <<"\n"; + exit(-1); + } + SNPatChr& snpatchr = snpingenome.SNP_atChr(index_chr); + int n = snpatchr.getSize(); + std::cout << "Size snpatchar: " << n << std::endl; + + std::vector SNPs_positions; + std::vector BAF_per_SNPs; + + for (int i = 0; i < n; i++) { + float value = snpatchr.getValueAt(i); + if ((value >= 0) && (snpatchr.getStatusAt(i)!=0)) { + int position = snpatchr.getPositionAt(i); + SNPs_positions.push_back(position); + BAF_per_SNPs.push_back(value); + } + } + std::cout << "Size ratio per SNP (not the attribute): " << BAF_per_SNPs.size() << std::endl; + + int j = 0; + int start = 0; + int end = 0; + for (int i = 0; i < (length_ - 1); i++) { + int n_values_in_window = 0; + while((SNPs_positions[j] >= (coordinates_[i]+1)) & (SNPs_positions[j] <= coordinates_[i+1])) { + if((ratio_[i] != -1) && (ratio_[i] < 3)) { + SNPs_positions_.push_back(SNPs_positions[j]); + BAF_per_SNPs_.push_back(BAF_per_SNPs[j]); + ratio_per_SNPs_.push_back(ratio_[i]); + median_ratio_per_SNPs_.push_back(medianProfile_[i]); + n_values_in_window += 1; + } + j += 1; + } + + // Calculate fragment length + if (median_ratio_per_SNPs_.size() > n_values_in_window) { + if (median_ratio_per_SNPs_.rbegin()[0] != median_ratio_per_SNPs_.rbegin()[n_values_in_window]) { + end = median_ratio_per_SNPs_.size() - n_values_in_window; + int frag_length = end - start; + fragment_lengths_per_snps_pos_.push_back(frag_length); + start = end; + } + } + } + + int frag_length = median_ratio_per_SNPs_.size() - start; + fragment_lengths_per_snps_pos_.push_back(frag_length); + std::cout << "Size of ratio per SNPS: " << ratio_per_SNPs_.size() << std::endl; + std::cout << "Size of list of fragments sizes: " << fragment_lengths_per_snps_pos_.size() << std::endl; +} + +/* +void ChrCopyNumber::transformBAFtoMAF() +{ + unsigned int n = BAF_in_window_.size(); + //MAF_in_window_(n); + for (unsigned int i = 0; i < n; i++) { + if (BAF_in_window_[i] == -1) { + MAF_in_window_.push_back(-1); + } else { + MAF_in_window_.push_back(std::abs(0.5 - BAF_in_window_[i]) + 0.5); + } + } +} +*/ +void ChrCopyNumber::transformBAFtoMAF() +{ + unsigned int n = BAF_per_SNPs_.size(); + MAF_per_SNPs_.resize(n); + for (unsigned int i = 0; i < n; i++) { + if (BAF_per_SNPs_[i] == -1) { + MAF_per_SNPs_[i] = -1; + } else { + MAF_per_SNPs_[i] = std::abs(0.5 - BAF_per_SNPs_[i]) + 0.5; + } + } +} + +void ChrCopyNumber::smoothRatioBySegments() { + std::cout << "Start smoothing ratio by segments" << std::endl; + int start = 0; + int last = 0; + int n = ratio_per_SNPs_.size(); + smoothed_ratio_.reserve(n); + for (unsigned int i = 0; i < fragment_lengths_per_snps_pos_.size(); i++) { + last += fragment_lengths_per_snps_pos_[i]; + std::vector segment; + std::vector med_seg; + if ((last - start) == 1) { + segment.push_back(ratio_per_SNPs_[start]); + } else { + segment = {ratio_per_SNPs_.begin() + start, ratio_per_SNPs_.begin() + last}; + med_seg = {median_ratio_per_SNPs_.begin() + start, median_ratio_per_SNPs_.begin() + last}; + } + simpleExponentialSmoothingRatio(segment, start, last); + start = last; + } + std::cout << "Size of smoothed ratio: " << smoothed_ratio_.size() << std::endl; +} + +void ChrCopyNumber::simpleExponentialSmoothingRatio(const std::vector& segment, int start, int last) +{ + std::cout << "Simple exponential smoothing from " << start << " to " << last << std::endl; + unsigned int n = segment.size(); + if (start == last){ + std::cout << "Skipping smoothing since the segment starts and ends at the same position: " << start << std::endl; + } else { + double alpha = 0.05; + smoothed_ratio_.push_back(segment[0]); + if (n > 1) { + smoothed_ratio_.push_back(segment[1]); + } + if (n > 2) { + for (unsigned int i = 2; i < n; i++) { + if (segment[i] == -1) { + smoothed_ratio_.push_back(-1); + } else { + if (segment[i-1] == -1) { + smoothed_ratio_.push_back(segment[i]); + int j = i - 2; + bool stop = false; + while ((j >= 0) && (stop == false)) { + if (segment[j] != -1) { + smoothed_ratio_[start + i] = alpha * segment[i] + (1 - alpha) * smoothed_ratio_[start + j]; + stop = true; + } + j -= 1; + } + } else { + smoothed_ratio_.push_back(alpha * segment[i] + (1 - alpha) * smoothed_ratio_[start + i - 1]); + } + } + } + } + } +} + +void ChrCopyNumber::rescaleRatio(float peak) +{ + std::cout << "Rescale ratio" << std::endl; + //float peak = findMaximumPeak(); + //std::cout << "Peak: " << peak << std::endl; + int n = smoothed_ratio_.size(); + if (peak != 0) { + for (int i = 0; i < n; i++) { + sm_rs_ratio_.push_back(smoothed_ratio_[i]/peak); + } + } else { + sm_rs_ratio_ = smoothed_ratio_; + } +} + +/* +float ChrCopyNumber::findMaximumPeak() +{ + int n = smoothed_ratio_.size(); + float max_el = *max_element(smoothed_ratio_.begin(), smoothed_ratio_.end()); + std::vector bins(ceil((max_el+0.01)/0.01)); + float x = 0; + std::generate(bins.begin(), bins.end(), [&]{return x+=0.01;}); + std::vector filt_smoothed_ratio; + for (int i = 0; i < n; i++) { + if (smoothed_ratio_[i] != -1) { + filt_smoothed_ratio.push_back(smoothed_ratio_[i]); + } + } + std::vector counts = makeHistogramOfCounts(filt_smoothed_ratio, bins); + std::cout << "Counts: "; + for (float c : counts) { + std::cout << c << " "; + } + std::cout << std::endl; + std::map peaks = findPeaks(counts, 2, 50, 20); + int peak_pos = 0; + float peak_value = 0; + for (std::map::iterator it = peaks.begin(); it != peaks.end(); ++it) { + if (it->second > peak_value) { + peak_value = it->second; + peak_pos = it->first; + } + } + float peak = bins[peak_pos]; + return peak; +} + */ + +void ChrCopyNumber::simpleExponentialSmoothingMAF() +{ + std::cout << "Start simple exponential smoothing on MAF" << std::endl; + float alpha = 0.05; + int n = MAF_per_SNPs_.size(); + std::cout << "/* MAF_per_SNPs_.size():\t" << n << std::endl; + if (n==0) { + return; + } + smoothed_MAF_.resize(n); + smoothed_MAF_[0] = MAF_per_SNPs_[0]; + for (unsigned int i = 1; i < n; i++) { + if (MAF_per_SNPs_[i] == -1) { + smoothed_MAF_[i] = -1; + } else { + if (MAF_per_SNPs_[i-1] == -1) { + smoothed_MAF_[i] = MAF_per_SNPs_[i]; + int j = i - 2; + bool stop = false; + while((j >= 0) && (stop == false)) { + if (smoothed_MAF_[j] != -1) { + smoothed_MAF_[i] = alpha * MAF_per_SNPs_[i] + (1 - alpha) * smoothed_MAF_[j]; + stop = true; + } + j--; + } + } else { + smoothed_MAF_[i] = alpha * MAF_per_SNPs_[i] + (1 - alpha) * smoothed_MAF_[i-1]; + } + } + } +} + +void ChrCopyNumber::filterRatioAndMAF() +{ + std::cout << "Filter BAF and ratio" << std::endl; + int n = sm_rs_ratio_.size(); + for (unsigned int i = 0; i < n; i++) { + if ((sm_rs_ratio_[i] != -1) && (sm_rs_ratio_[i] < 3) && (smoothed_MAF_[i] != -1)) { + filtered_ratio_.push_back(sm_rs_ratio_[i]); + filtered_MAF_.push_back(smoothed_MAF_[i]); + } + } + std::cout << "Size of filtered ratio: " << filtered_ratio_.size() << std::endl; +} + +float ChrCopyNumber::getSmoothedRatioAtBin(int i) { + return smoothed_ratio_[i]; +} + +int ChrCopyNumber::getSmoothedRatioSize() { + return smoothed_ratio_.size(); +} + +float ChrCopyNumber::getRescaledRatioAtBin(int i) { + return sm_rs_ratio_[i]; +} + +float ChrCopyNumber::getFilteredRatioAt(int i) { + return filtered_ratio_[i]; +} + +float ChrCopyNumber::getRatioPerSNPat(int i) { + return ratio_per_SNPs_[i]; +} + +float ChrCopyNumber::getBAFPerSNPat(int i) { + return BAF_per_SNPs_[i]; +} + +float ChrCopyNumber::getMAFPerSNPat(int i) { + return MAF_per_SNPs_[i]; +} + +float ChrCopyNumber::getMedianRatioPerSNPat(int i) { + return median_ratio_per_SNPs_[i]; +} + +float ChrCopyNumber::getSmoothedMAFat(int i) { + return smoothed_MAF_[i]; +} + +float ChrCopyNumber::getFilteredMAFat(int i) { + return filtered_MAF_[i]; +} + +int ChrCopyNumber::getSNPLength() { + return ratio_per_SNPs_.size(); +} + +int ChrCopyNumber::getFilteredLength() { + return filtered_ratio_.size(); +} + +float ChrCopyNumber::getSampledBAFat(int i) { + return BAF_in_window_[i]; +} + +float ChrCopyNumber::getSampledMAFat(int i) { + return MAF_in_window_[i]; +} + +int ChrCopyNumber::getSNPPositionAt(int i) { + return SNPs_positions_[i]; +} + + +//using namespace std; diff --git a/src/ChrCopyNumber.h b/src/ChrCopyNumber.h index 13e1833..a16ecb7 100644 --- a/src/ChrCopyNumber.h +++ b/src/ChrCopyNumber.h @@ -153,7 +153,39 @@ class ChrCopyNumber void setLookingForSubclones(bool); float getSmoothedForInterval(int start , int end); -private: + // Added by Gara + // For each window, if there is more than one BAF, uniformly sample one BAF + void createRatioAndBAFFromSNPs(SNPinGenome& snpingenome); + void transformBAFtoMAF(); + // SES of copy number ratios that are on the same segment. Segment: piece of genome that has the same median ratio + void smoothRatioBySegments(); + // Simple exponential smoothing for ratio and MAF + void simpleExponentialSmoothingRatio(const std::vector& segment, int start, int last); + void simpleExponentialSmoothingMAF(); + // Rescale the ratio by the location of the highest peak + //float findMaximumPeak(); + void rescaleRatio(float peak); + // Simultaneously filter ratio and MAF in order to get rid of -1 values and in order for the two vectors to have the same length + void filterRatioAndMAF(); + // For printing + float getSmoothedRatioAtBin(int i); + float getRescaledRatioAtBin(int i); + float getRatioPerSNPat(int i); + float getBAFPerSNPat(int i); + float getMAFPerSNPat(int i); + float getSmoothedMAFat(int i); + float getMedianRatioPerSNPat(int i); + float getFilteredRatioAt(int i); + float getFilteredMAFat(int i); + int getSNPLength(); + int getFilteredLength(); + float getSampledBAFat(int i); + float getSampledMAFat(int i); + int getSNPPositionAt(int i); + + int getSmoothedRatioSize(); + + private: // std::vector coordinatesTmp_; // std::vector endsTmp_; // std::vector chr_namestmp; @@ -200,6 +232,21 @@ class ChrCopyNumber std::vector BAFsymbPerFrag_; //estimation of BAF for each segment: AA,AAB;AB,AABB etc - one value per fragment std::vector estBAFuncertaintyPerFrag_;//uncertainty of estimation of BAF for each segment (1./(LL_best-LL_secondBest))) - one value per fragment + // Added by Gara + std::vector BAF_in_window_; + std::vector MAF_in_window_; + std::vector BAF_per_SNPs_; + std::vector MAF_per_SNPs_; + std::vector ratio_per_SNPs_; + std::vector smoothed_ratio_; + std::vector smoothed_MAF_; + std::vector sm_rs_ratio_; + std::vector filtered_ratio_; + std::vector filtered_MAF_; + std::vector fragment_lengths_per_snps_pos_; + std::vector median_ratio_per_SNPs_; + std::vector SNPs_positions_; + }; #endif diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp index 3a03107..00695db 100644 --- a/src/GenomeCopyNumber.cpp +++ b/src/GenomeCopyNumber.cpp @@ -25,58 +25,61 @@ using namespace std ; GenomeCopyNumber::GenomeCopyNumber(void) { - ploidy_ = NA; - step_=NA; - hasBAF_=0; - ifUsedControl_ = false; - normalContamination_=0; - sex_=""; - SeekingSubc_ = false; - isMappUsed_=false; - totalNumberOfPairs_=0; - normalNumberOfPairs_=0; + ploidy_ = NA; + step_=NA; + hasBAF_=0; + ifUsedControl_ = false; + normalContamination_=0; + sex_=""; + SeekingSubc_ = false; + isMappUsed_=false; + totalNumberOfPairs_=0; + normalNumberOfPairs_=0; + dataSubsamplingRateInPuritySearch = 1000; + dataSubsamplingRateInPloidyEvaluation = 50; + doRescaleRatio=true; } bool GenomeCopyNumber::isMappUsed() {return isMappUsed_;} void GenomeCopyNumber::readCopyNumber(std::string const& mateFileName ,std::string const& inputFormat, std::string const& matesOrientation, std::string const& chrLenFileName, float coefficientOfVariation ) { - //first get the number of reads and the genome size - //long genomeSize = 0; - long readNumber = 0; - int windowSize; - //reading the file with genome information - std::vector names; - std::vector lengths; - readFileWithGenomeInfo(chrLenFileName, names, lengths); - refGenomeSize_ = sum(lengths); - cout << "\t total genome size:\t" << refGenomeSize_ << "\n"; - if ((inputFormat.compare("pileup")==0 || inputFormat.compare("SAMtools pileup")==0)) { - readNumber = getReadNumberFromPileup(mateFileName); - } else { - readNumber = getLineNumber(mateFileName, pathToReference_, pathToSamtools_, pathToSambamba_, SambambaThreads_); - } - cout << "\t read number:\t" << readNumber << "\n"; - cout << "\t coefficientOfVariation:\t" << coefficientOfVariation << "\n"; - windowSize = round_f(float(1./(coefficientOfVariation*coefficientOfVariation)/readNumber*refGenomeSize_)); - cout << "\t evaluated window size:\t" << windowSize << "\n"; - for (int i = 0; i < (int) names.size(); i++) { - ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i]); - chromosomesInd_.insert(pair (names[i],i)); - chrCopyNumber_.push_back(chrCopyNumber); - } - //cout << "data structure created"; - //read mateFileName and calculate copyNumber + //first get the number of reads and the genome size + //long genomeSize = 0; + long readNumber = 0; + int windowSize; + //reading the file with genome information + std::vector names; + std::vector lengths; + readFileWithGenomeInfo(chrLenFileName, names, lengths); + refGenomeSize_ = sum(lengths); + cout << "\t total genome size:\t" << refGenomeSize_ << "\n"; + if ((inputFormat.compare("pileup")==0 || inputFormat.compare("SAMtools pileup")==0)) { + readNumber = getReadNumberFromPileup(mateFileName); + } else { + readNumber = getLineNumber(mateFileName, pathToReference_, pathToSamtools_, pathToSambamba_, SambambaThreads_); + } + cout << "\t read number:\t" << readNumber << "\n"; + cout << "\t coefficientOfVariation:\t" << coefficientOfVariation << "\n"; + windowSize = round_f(float(1./(coefficientOfVariation*coefficientOfVariation)/readNumber*refGenomeSize_)); + cout << "\t evaluated window size:\t" << windowSize << "\n"; + for (int i = 0; i < (int) names.size(); i++) { + ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i]); + chromosomesInd_.insert(pair (names[i],i)); + chrCopyNumber_.push_back(chrCopyNumber); + } + //cout << "data structure created"; + //read mateFileName and calculate copyNumber - GenomeCopyNumber::fillMyHash(mateFileName ,inputFormat, matesOrientation, windowSize, windowSize); + GenomeCopyNumber::fillMyHash(mateFileName ,inputFormat, matesOrientation, windowSize, windowSize); } long GenomeCopyNumber::getNormalNumberOfPairs(void) { - return normalNumberOfPairs_; + return normalNumberOfPairs_; } int GenomeCopyNumber::getWindowSize(void) { - return windowSize_; + return windowSize_; } void GenomeCopyNumber::setStep(int step) { @@ -86,8 +89,8 @@ void GenomeCopyNumber::setStep(int step) { void GenomeCopyNumber::setNormalContamination(float normalContamination) { normalContamination_=normalContamination; vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) - it->setNormalContamination(normalContamination); + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) + it->setNormalContamination(normalContamination); } bool GenomeCopyNumber::ifHasBAF() { @@ -123,11 +126,11 @@ void GenomeCopyNumber::setBAFtrue() { } void GenomeCopyNumber::readCopyNumber(std::string const& mateFileName ,std::string const& inputFormat, std::string const& matesOrientation, std::string const& chrLenFileName, - int windowSize , int step, std::string targetBed ) { + int windowSize , int step, std::string targetBed ) { if (WESanalysis == false) { if (step == NA) step = windowSize; - //check if step value is correct: + //check if step value is correct: if (step <= 0 || step > windowSize) { cerr << "step should be a positive interger value less than or equal to the window size\n"; exit(-1); @@ -138,20 +141,20 @@ void GenomeCopyNumber::readCopyNumber(std::string const& mateFileName ,std::stri step_ = step; } - //reading the file with genome information - std::vector names; - std::vector lengths; - readFileWithGenomeInfo(chrLenFileName, names, lengths); - refGenomeSize_ = sum(lengths); - for (int i = 0; i < (int) names.size(); i++) { - ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step, targetBed); - chromosomesInd_.insert(pair (names[i],i)); - chrCopyNumber_.push_back(chrCopyNumber); - } - //read mateFileName and calculate copyNumber + //reading the file with genome information + std::vector names; + std::vector lengths; + readFileWithGenomeInfo(chrLenFileName, names, lengths); + refGenomeSize_ = sum(lengths); + for (int i = 0; i < (int) names.size(); i++) { + ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step, targetBed); + chromosomesInd_.insert(pair (names[i],i)); + chrCopyNumber_.push_back(chrCopyNumber); + } + //read mateFileName and calculate copyNumber - GenomeCopyNumber::fillMyHash(mateFileName ,inputFormat, matesOrientation, windowSize, step, targetBed); + GenomeCopyNumber::fillMyHash(mateFileName ,inputFormat, matesOrientation, windowSize, step, targetBed); //remove chromosomes that do to have reads or exons: @@ -174,79 +177,79 @@ void GenomeCopyNumber::readCopyNumber(std::string const& mateFileName ,std::stri void GenomeCopyNumber::initCopyNumber(std::string const& chrLenFileName, int windowSize , int step, std::string targetBed) { - ThreadPoolManager::getInstance()->lock(); - if (WESanalysis == false) { - if (step == NA) { - step = windowSize; - } - //check if steo value is correct: - if (step <= 0 || step > windowSize) { - cerr << "step should be a positive interger value less than or equal to the window size\n"; - exit(-1); + ThreadPoolManager::getInstance()->lock(); + if (WESanalysis == false) { + if (step == NA) { + step = windowSize; + } + //check if steo value is correct: + if (step <= 0 || step > windowSize) { + cerr << "step should be a positive interger value less than or equal to the window size\n"; + exit(-1); + } + step_=step; + windowSize_ = windowSize; + //reading the file with genome information + std::vector names; + std::vector lengths; + readFileWithGenomeInfo(chrLenFileName, names, lengths); + refGenomeSize_ = sum(lengths); + for (int i = 0; i < (int) names.size(); i++) { + ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step); + chromosomesInd_.insert(pair (names[i],i)); + chrCopyNumber_.push_back(chrCopyNumber); + } + } else { + std::vector names; + std::vector lengths; + readFileWithGenomeInfo(chrLenFileName, names, lengths); + refGenomeSize_ = sum(lengths); + for (int i = 0; i < (int) names.size(); i++) { + ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step, targetBed); + chromosomesInd_.insert(pair (names[i],i)); + chrCopyNumber_.push_back(chrCopyNumber); + } } - step_=step; - windowSize_ = windowSize; - //reading the file with genome information - std::vector names; - std::vector lengths; - readFileWithGenomeInfo(chrLenFileName, names, lengths); - refGenomeSize_ = sum(lengths); - for (int i = 0; i < (int) names.size(); i++) { - ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step); - chromosomesInd_.insert(pair (names[i],i)); - chrCopyNumber_.push_back(chrCopyNumber); - } - } else { - std::vector names; - std::vector lengths; - readFileWithGenomeInfo(chrLenFileName, names, lengths); - refGenomeSize_ = sum(lengths); - for (int i = 0; i < (int) names.size(); i++) { - ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step, targetBed); - chromosomesInd_.insert(pair (names[i],i)); - chrCopyNumber_.push_back(chrCopyNumber); - } - } - ThreadPoolManager::getInstance()->unlock(); + ThreadPoolManager::getInstance()->unlock(); } void GenomeCopyNumber::finishCopyNumber(long normalCount) { - totalNumberOfPairs_ = normalCount; - normalNumberOfPairs_ = normalCount; - cout << normalNumberOfPairs_<< " reads used to compute copy number profile\n"; + totalNumberOfPairs_ = normalCount; + normalNumberOfPairs_ = normalCount; + cout << normalNumberOfPairs_<< " reads used to compute copy number profile\n"; } long GenomeCopyNumber::getTotalNumberOfPairs() { - return totalNumberOfPairs_; + return totalNumberOfPairs_; } void GenomeCopyNumber::calculateBreakpoints(double breakPointThreshold, int breakPointType) { - cout << "..Calculating breakpoints, breakPointThreshold = " <newThreadPool("ChrCopyNumber_calculateBreakpoint"); - for (vector::iterator it = chrCopyNumber_.begin(); it != chrCopyNumber_.end(); it++) { - ChrCopyNumber& chrCopyNumber = *it; - ChrCopyNumberCalculateBreakpointArgWrapper* bkpArg = new ChrCopyNumberCalculateBreakpointArgWrapper(chrCopyNumber, breakPointThreshold, breakPointType); - thrPool->addThread(ChrCopyNumber_calculateBreakpoint_wrapper, bkpArg); - } + cout << "..Calculating breakpoints, breakPointThreshold = " <newThreadPool("ChrCopyNumber_calculateBreakpoint"); + for (vector::iterator it = chrCopyNumber_.begin(); it != chrCopyNumber_.end(); it++) { + ChrCopyNumber& chrCopyNumber = *it; + ChrCopyNumberCalculateBreakpointArgWrapper* bkpArg = new ChrCopyNumberCalculateBreakpointArgWrapper(chrCopyNumber, breakPointThreshold, breakPointType); + thrPool->addThread(ChrCopyNumber_calculateBreakpoint_wrapper, bkpArg); + } - thrPool->run(); - delete thrPool; + thrPool->run(); + delete thrPool; } void GenomeCopyNumber::calculateBAFBreakpoints(double breakPointThreshold, int breakPointType) { - cout << "..Calculating breakpoints for BAF, breakPointThreshold = " <newThreadPool("ChrCopyNumber_calculateBAFBreakpoint"); - for (vector::iterator it = chrCopyNumber_.begin(); it != chrCopyNumber_.end(); it++) { - ChrCopyNumber& chrCopyNumber = *it; - ChrCopyNumberCalculateBreakpointArgWrapper* bkpArg = new ChrCopyNumberCalculateBreakpointArgWrapper(chrCopyNumber, breakPointThreshold, breakPointType); - thrPool->addThread(ChrCopyNumber_calculateBAFBreakpoint_wrapper, bkpArg); - } + ThreadPool* thrPool = ThreadPoolManager::getInstance()->newThreadPool("ChrCopyNumber_calculateBAFBreakpoint"); + for (vector::iterator it = chrCopyNumber_.begin(); it != chrCopyNumber_.end(); it++) { + ChrCopyNumber& chrCopyNumber = *it; + ChrCopyNumberCalculateBreakpointArgWrapper* bkpArg = new ChrCopyNumberCalculateBreakpointArgWrapper(chrCopyNumber, breakPointThreshold, breakPointType); + thrPool->addThread(ChrCopyNumber_calculateBAFBreakpoint_wrapper, bkpArg); + } - thrPool->run(); - delete thrPool; + thrPool->run(); + delete thrPool; #else - vector::iterator it=chrCopyNumber_.begin(); + vector::iterator it=chrCopyNumber_.begin(); //calculate breakpoints for the first chromosome and get its length to normalize other graphs int firstChromLen = 0; //we don't know it if (it != chrCopyNumber_.end()) { @@ -268,38 +271,38 @@ void GenomeCopyNumber::calculateBAFBreakpoints(double breakPointThreshold, int b } void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string const& inputFormat_str, std::string const& matesOrientation_str, int windowSize , int step, std::string targetBed) { - //read mateFileName and calculate copyNumber - long count = 0; - long normalCount = 0; - int bin = 0; - - cout << "..[genomecopynumber] Starting reading "<< mateFileName << "\n"; - //if (mateFileName.substr(mateFileName.size()-1,3).compare(".gz")==0) { - // igzstream in( mateFileName ); - // if ( ! in.good()) { - // std::cerr << "ERROR: Opening file `" << mateFileName << "' failed.\n"; - // return EXIT_FAILURE; - // } - // in.close(); - //} - std::ifstream fileMates (mateFileName.c_str()); - vector insertSizeVector; - windowSize_ = windowSize; - step_=step; - string line; - if (!fileMates.is_open()) { - cerr << "Error: unable to open "+mateFileName+"\n" ; - exit(-1); - } + //read mateFileName and calculate copyNumber + long count = 0; + long normalCount = 0; + int bin = 0; + + cout << "..[genomecopynumber] Starting reading "<< mateFileName << "\n"; + //if (mateFileName.substr(mateFileName.size()-1,3).compare(".gz")==0) { + // igzstream in( mateFileName ); + // if ( ! in.good()) { + // std::cerr << "ERROR: Opening file `" << mateFileName << "' failed.\n"; + // return EXIT_FAILURE; + // } + // in.close(); + //} + std::ifstream fileMates (mateFileName.c_str()); + vector insertSizeVector; + windowSize_ = windowSize; + step_=step; + string line; + if (!fileMates.is_open()) { + cerr << "Error: unable to open "+mateFileName+"\n" ; + exit(-1); + } #ifdef PROFILE_TRACE - time_t t0 = time(NULL); + time_t t0 = time(NULL); #endif - MateOrientation matesOrientation = getMateOrientation(matesOrientation_str); + MateOrientation matesOrientation = getMateOrientation(matesOrientation_str); - InputFormat inputFormat; - char* line_buffer; + InputFormat inputFormat; + char* line_buffer; if (inputFormat_str.compare("bam")==0 || inputFormat_str.compare("BAM")==0 || mateFileName.substr(mateFileName.size()-4,4).compare(".bam")==0 || mateFileName.substr(mateFileName.size()-3,3).compare(".gz")==0) { fileMates.close(); @@ -310,97 +313,97 @@ void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string c string myInputFormat=inputFormat_str; if (mateFileName.substr(mateFileName.size()-3,3).compare(".gz")!=0) { - if (mateFileName.substr(mateFileName.size()-4,4).compare(".bam")==0) { + if (mateFileName.substr(mateFileName.size()-4,4).compare(".bam")==0) { if (pathToSambamba_ != "") - { + { command = pathToSambamba_ + " view -t " + SambambaThreads_ + " " + mateFileName; myInputFormat="sam"; //will try to use existing sambamba //cout << "..sambamba should be installed to be able to read BAM files; will use the following command for sambamba: "<second; + if (chromosomesInd_.find(chr) == chromosomesInd_.end()) {return NA;} + return chromosomesInd_.find(chr)->second; } void GenomeCopyNumber::recalculateRatio (float contamination) { - if (contamination >= 1 || contamination <= 0) { + if (contamination >= 1 || contamination <= 0) { cerr << "contamination should be between 0 and 1\n"; exit(-1); - } - vector::iterator it; + } + vector::iterator it; for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { //should take into account that normally one has only one copy of X and Y.. it->recalculateRatioWithContam(contamination,0.5, isRatioLogged_); - } else + } else it->recalculateRatioWithContam(contamination,1, isRatioLogged_); - } + } } void GenomeCopyNumber::recalculateRatioUsingCG (int degree, bool intercept, float minExpectedGC, float maxExpectedGC) { - if (degree > MAXDEGREE) { + if (degree > MAXDEGREE) { cerr << "polynomial degree should be < 10\n"; exit (-1); - } - int maximalNumberOfCopies = ploidy_*2; - float interval = float (0.01) ; - - //first guess about parameters - const int npoints = degree+2; - - - double around [MAXDEGREE+2]; - for (int i = 0; i=0; j--) { - xy(i,j)=xy(i,j+1)*around[i]; - } - /* this is equal to - xy(i,0) = around[i]*around[i]*around[i]; - xy(i,1) = around[i]*around[i]; - xy(i,2) = around[i]; - xy(i,3) = yValues[i]; */ - } - linearmodel lm; - int info; - lrreport ar; + } + int maximalNumberOfCopies = ploidy_*2; + float interval = float (0.01) ; + + //first guess about parameters + const int npoints = degree+2; + + + double around [MAXDEGREE+2]; + for (int i = 0; i=0; j--) { + xy(i,j)=xy(i,j+1)*around[i]; + } + /* this is equal to + xy(i,0) = around[i]*around[i]*around[i]; + xy(i,1) = around[i]*around[i]; + xy(i,2) = around[i]; + xy(i,3) = yValues[i]; */ + } + linearmodel lm; + int info; + lrreport ar; if (intercept) lrbuild(xy,npoints,nvars,info,lm,ar); - else - lrbuildz(xy,npoints,nvars,info,lm,ar); - if (info != 1) { - cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; - } - ap::real_1d_array v; + else + lrbuildz(xy,npoints,nvars,info,lm,ar); + if (info != 1) { + cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; + } + ap::real_1d_array v; v.setlength(nvars+int(intercept)); - lrunpack(lm,v,nvars); - //cout << v(0) << "\t" << v(1)<< "\t" < y; //y ~ ax^2+bx+c - vector x; - - //fill x and y: - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - //use a threshold, but correct using notN profile + a[degree] = v(degree); + else + a[degree] = 0; + + vector y; //y ~ ax^2+bx+c + vector x; + + //fill x and y: + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { + //use a threshold, but correct using notN profile if (it->getMappabilityLength()>0) { for (int i = 0; i< it->getLength(); i++) { if ((it->getRatioAtBin(i)>0)&&(it->getMappabilityProfileAt(i)>minMappabilityPerWindow)) { @@ -530,50 +533,50 @@ void GenomeCopyNumber::recalculateRatioUsingCG (int degree, bool intercept, floa } } - } - int maximalNumberOfIterations = 100; - float rmserror = runEM(x,y,a,degree,maximalNumberOfIterations,ploidy_,maximalNumberOfCopies, intercept, normalContamination_); - if (rmserror == -1) { - cerr << "Error in EM => unable to calculate normalized profile\n"; - return; - } - cout << "root mean square error = " << rmserror << "\n"; - if (degree == 3) { - cout << "Y = " << a[0] << "*x*x*x+" << a[1] << "*x*x+" << a[2] << "*x+" << a[3] <<"\n"; - }else if (degree == 2) { - cout << "Y = " << a[0] << "*x*x+" << a[1] << "*x+" << a[2] <<"\n"; - }else if (degree == 1) { - cout << "Y = " << a[0] << "*x+" << a[1] << "\n"; - } - if (degree > 3) { + } + int maximalNumberOfIterations = 100; + float rmserror = runEM(x,y,a,degree,maximalNumberOfIterations,ploidy_,maximalNumberOfCopies, intercept, normalContamination_); + if (rmserror == -1) { + cerr << "Error in EM => unable to calculate normalized profile\n"; + return; + } + cout << "root mean square error = " << rmserror << "\n"; + if (degree == 3) { + cout << "Y = " << a[0] << "*x*x*x+" << a[1] << "*x*x+" << a[2] << "*x+" << a[3] <<"\n"; + }else if (degree == 2) { + cout << "Y = " << a[0] << "*x*x+" << a[1] << "*x+" << a[2] <<"\n"; + }else if (degree == 1) { + cout << "Y = " << a[0] << "*x+" << a[1] << "\n"; + } + if (degree > 3) { cout << "Y = "; for (int i=0; irecalculateRatio(a,degree); - } + } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->recalculateRatio(a,degree); + } } void GenomeCopyNumber::setAllNormal () { - vector::iterator it; + vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - it->setAllNormal(); - } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->setAllNormal(); + } } int GenomeCopyNumber::calculateRatioUsingCG (bool intercept, float minExpectedGC, float maxExpectedGC) { //returns 1 if the number of iteration is less than max; otherwise 0 - //try degree 3 and 4, SELECT THE ONE WITH LESS ITTERATIONS: + //try degree 3 and 4, SELECT THE ONE WITH LESS ITTERATIONS: int minDegreeToTest = 3; int maxDegreeToTest = 4; int selectedDegree=minDegreeToTest; int maximalNumberOfIterations = 300; int bestNumberOfIterations=maximalNumberOfIterations; - // int bestSqareError=INFINITY; + // int bestSqareError=INFINITY; int valueToReturn = 0; @@ -591,40 +594,40 @@ int GenomeCopyNumber::calculateRatioUsingCG (bool intercept, float minExpectedGC //fill x and y: for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (countAutosomes>0 && !(it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos) || countAutosomes==0) { - // if uniqueMatch, do correction to mappability - if (uniqueMatch) { - //use mappabilityProfile_ and correct + if (countAutosomes>0 && !(it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos) || countAutosomes==0) { + // if uniqueMatch, do correction to mappability + if (uniqueMatch) { + //use mappabilityProfile_ and correct + for (int i = 0; i< it->getLength(); i++) { + if ((it->getValueAt(i)>0)&&(it->getMappabilityProfileAt(i)>minMappabilityPerWindow)) { + x.push_back(it->getCGprofileAt(i)); + y.push_back(it->getValueAt(i)/it->getMappabilityProfileAt(i)); + } + } + } else { + //use a threshold, but correct using notN profile + if (it->getMappabilityLength()>0) { for (int i = 0; i< it->getLength(); i++) { if ((it->getValueAt(i)>0)&&(it->getMappabilityProfileAt(i)>minMappabilityPerWindow)) { x.push_back(it->getCGprofileAt(i)); - y.push_back(it->getValueAt(i)/it->getMappabilityProfileAt(i)); + y.push_back(it->getValueAt(i)/it->getNotNprofileAt(i)); } } } else { - //use a threshold, but correct using notN profile - if (it->getMappabilityLength()>0) { - for (int i = 0; i< it->getLength(); i++) { - if ((it->getValueAt(i)>0)&&(it->getMappabilityProfileAt(i)>minMappabilityPerWindow)) { - x.push_back(it->getCGprofileAt(i)); - y.push_back(it->getValueAt(i)/it->getNotNprofileAt(i)); - } - } - } else { - for (int i = 0; i< it->getLength(); i++) { - if ((it->getValueAt(i)>0)&&(it->getNotNprofileAt(i)>minMappabilityPerWindow)) { - x.push_back(it->getCGprofileAt(i)); - y.push_back(it->getValueAt(i)/it->getNotNprofileAt(i)); - } + for (int i = 0; i< it->getLength(); i++) { + if ((it->getValueAt(i)>0)&&(it->getNotNprofileAt(i)>minMappabilityPerWindow)) { + x.push_back(it->getCGprofileAt(i)); + y.push_back(it->getValueAt(i)/it->getNotNprofileAt(i)); } } } } + } } for (int degree=minDegreeToTest;degree<=maxDegreeToTest; degree++) { if (degree > MAXDEGREE) { - break; + break; } int maximalNumberOfCopies = ploidy_*2; float interval = float (0.01) ; @@ -674,7 +677,7 @@ int GenomeCopyNumber::calculateRatioUsingCG (bool intercept, float minExpectedGC //cout << v(0) << "\t" << v(1)<< "\t" < MAXDEGREE) { + if (degree > MAXDEGREE) { cerr << "polynomial degree should be < 10\n"; exit (-1); - } - int maximalNumberOfCopies = ploidy_*2; - float interval = float (0.01) ; - - //first guess about parameters - const int npoints = degree+2; - - - double around [MAXDEGREE+2]; - for (int i = 0; i=0; j--) { - xy(i,j)=xy(i,j+1)*around[i]; - } - /* this is equal to - xy(i,0) = around[i]*around[i]*around[i]; - xy(i,1) = around[i]*around[i]; - xy(i,2) = around[i]; - xy(i,3) = yValues[i]; */ - } - linearmodel lm; - int info; - lrreport ar; + } + int maximalNumberOfCopies = ploidy_*2; + float interval = float (0.01) ; + + //first guess about parameters + const int npoints = degree+2; + + + double around [MAXDEGREE+2]; + for (int i = 0; i=0; j--) { + xy(i,j)=xy(i,j+1)*around[i]; + } + /* this is equal to + xy(i,0) = around[i]*around[i]*around[i]; + xy(i,1) = around[i]*around[i]; + xy(i,2) = around[i]; + xy(i,3) = yValues[i]; */ + } + linearmodel lm; + int info; + lrreport ar; if (intercept) lrbuild(xy,npoints,nvars,info,lm,ar); - else - lrbuildz(xy,npoints,nvars,info,lm,ar); - if (info != 1) { - cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; - } - ap::real_1d_array v; + else + lrbuildz(xy,npoints,nvars,info,lm,ar); + if (info != 1) { + cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; + } + ap::real_1d_array v; v.setlength(nvars+int(intercept)); - lrunpack(lm,v,nvars); - //cout << v(0) << "\t" << v(1)<< "\t" < unable to calculate normalized profile\n"; - return 0; - } - cout << "root mean square error = " << rmserror << "\n"; - if (degree == 3) { - cout << "Y = " << a[0] << "*x*x*x+" << a[1] << "*x*x+" << a[2] << "*x+" << a[3] <<"\n"; - }else if (degree == 2) { - cout << "Y = " << a[0] << "*x*x+" << a[1] << "*x+" << a[2] <<"\n"; - }else if (degree == 1) { - cout << "Y = " << a[0] << "*x+" << a[1] << "\n"; - } + if (rmserror == -1) { + cerr << "Error in EM => unable to calculate normalized profile\n"; + return 0; + } + cout << "root mean square error = " << rmserror << "\n"; + if (degree == 3) { + cout << "Y = " << a[0] << "*x*x*x+" << a[1] << "*x*x+" << a[2] << "*x+" << a[3] <<"\n"; + }else if (degree == 2) { + cout << "Y = " << a[0] << "*x*x+" << a[1] << "*x+" << a[2] <<"\n"; + }else if (degree == 1) { + cout << "Y = " << a[0] << "*x+" << a[1] << "\n"; + } if (degree > 3) { cout << "Y = "; for (int i=0; icalculateRatio(a,degree); - } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->calculateRatio(a,degree); + } x.clear(); y.clear(); @@ -805,81 +808,81 @@ int GenomeCopyNumber::calculateRatioUsingCG (bool intercept, float minExpectedGC int GenomeCopyNumber::calculateRatioUsingCG (int degree, bool intercept, float minExpectedGC, float maxExpectedGC) { - if (degree > MAXDEGREE) { + if (degree > MAXDEGREE) { cerr << "polynomial degree should be < 10\n"; exit (-1); - } - int maximalNumberOfCopies = ploidy_*2; - float interval = float (0.01) ; + } + int maximalNumberOfCopies = ploidy_*2; + float interval = float (0.01) ; - //first guess about parameters - const int npoints = degree+2; + //first guess about parameters + const int npoints = degree+2; int valueToReturn = 0; - double around [MAXDEGREE+2]; - for (int i = 0; i=0; j--) { - xy(i,j)=xy(i,j+1)*around[i]; - } - /* this is equal to - xy(i,0) = around[i]*around[i]*around[i]; - xy(i,1) = around[i]*around[i]; - xy(i,2) = around[i]; - xy(i,3) = yValues[i]; */ - } - linearmodel lm; - int info; - lrreport ar; + double around [MAXDEGREE+2]; + for (int i = 0; i=0; j--) { + xy(i,j)=xy(i,j+1)*around[i]; + } + /* this is equal to + xy(i,0) = around[i]*around[i]*around[i]; + xy(i,1) = around[i]*around[i]; + xy(i,2) = around[i]; + xy(i,3) = yValues[i]; */ + } + linearmodel lm; + int info; + lrreport ar; if (intercept) lrbuild(xy,npoints,nvars,info,lm,ar); - else - lrbuildz(xy,npoints,nvars,info,lm,ar); - if (info != 1) { - cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; - } - ap::real_1d_array v; + else + lrbuildz(xy,npoints,nvars,info,lm,ar); + if (info != 1) { + cerr << "Error in the first linear regression (the first guess about parameters), code: " << info <<"\n"; + } + ap::real_1d_array v; v.setlength(nvars+int(intercept)); - lrunpack(lm,v,nvars); - //cout << v(0) << "\t" << v(1)<< "\t" < y; //y ~ ax^2+bx+c - vector x; + vector y; //y ~ ax^2+bx+c + vector x; - //fill x and y: - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + //fill x and y: + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { // if uniqueMatch, do correction to mappability - if (uniqueMatch) { + if (uniqueMatch) { //use mappabilityProfile_ and correct for (int i = 0; i< it->getLength(); i++) { if ((it->getValueAt(i)>0)&&(it->getMappabilityProfileAt(i)>minMappabilityPerWindow)) { @@ -887,7 +890,7 @@ int GenomeCopyNumber::calculateRatioUsingCG (int degree, bool intercept, float m y.push_back(it->getValueAt(i)/it->getMappabilityProfileAt(i)); } } - } else { + } else { //use a threshold, but correct using notN profile if (it->getMappabilityLength()>0) { for (int i = 0; i< it->getLength(); i++) { @@ -904,132 +907,132 @@ int GenomeCopyNumber::calculateRatioUsingCG (int degree, bool intercept, float m } } } - } + } } - } - int maximalNumberOfIterations = 300; - int realNumberOfIterations = maximalNumberOfIterations; + } + int maximalNumberOfIterations = 300; + int realNumberOfIterations = maximalNumberOfIterations; float rmserror = runEM(x,y,a,degree,realNumberOfIterations,ploidy_,maximalNumberOfCopies, intercept, normalContamination_); - if (rmserror == -1) { - cerr << "Error in EM => unable to calculate normalized profile\n"; - return 0; - } + if (rmserror == -1) { + cerr << "Error in EM => unable to calculate normalized profile\n"; + return 0; + } - if (realNumberOfIterations 3) { cout << "Y = "; for (int i=0; icalculateRatio(a,degree); - } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->calculateRatio(a,degree); + } x.clear(); y.clear(); return valueToReturn; } void GenomeCopyNumber::setPloidy(int ploidy) { - ploidy_ = ploidy; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) - it->setPloidy(ploidy); + ploidy_ = ploidy; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) + it->setPloidy(ploidy); } double GenomeCopyNumber::calculateMedianRatioAround (float interval, float around) { - float maxCG = around+interval; - float minCG = around-interval; - - vector myValuesAround; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) - for (int i = 0; i< it->getLength(); i++) { - if ((it->getCGprofileAt(i)<=maxCG)&&(it->getCGprofileAt(i)>=minCG)) - if (it->getRatioAtBin(i) >0) //non-zero values - myValuesAround.push_back(it->getRatioAtBin(i)); - } - } + float maxCG = around+interval; + float minCG = around-interval; + + vector myValuesAround; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) + for (int i = 0; i< it->getLength(); i++) { + if ((it->getCGprofileAt(i)<=maxCG)&&(it->getCGprofileAt(i)>=minCG)) + if (it->getRatioAtBin(i) >0) //non-zero values + myValuesAround.push_back(it->getRatioAtBin(i)); + } + } if (myValuesAround.size()==0) { cerr << "Error: zero reads in windows with the GC-content around "< myValues; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) - for (int i = 0; i< it->getLength(); i++) { - if (it->getValueAt(i) >0) //non-zero values + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) + for (int i = 0; i< it->getLength(); i++) { + if (it->getValueAt(i) >0) //non-zero values myValues.push_back(it->getValueAt(i)); - } - } + } + } if (myValues.size()==0) { - cerr << "Ersqrt(139000)ror: no windows with reads\n"; - cerr << "Unable to proceed..\n"; - exit(-1); + cerr << "Ersqrt(139000)ror: no windows with reads\n"; + cerr << "Unable to proceed..\n"; + exit(-1); } - float sd = get_sd(myValues,mean); - myValues.clear(); - return floor(sd); + float sd = get_sd(myValues,mean); + myValues.clear(); + return floor(sd); } int GenomeCopyNumber::calculateMedianReadCountPerWindow() { vector myValues; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) - for (int i = 0; i< it->getLength(); i++) { - if (it->getValueAt(i) >0) //non-zero values + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) + for (int i = 0; i< it->getLength(); i++) { + if (it->getValueAt(i) >0) //non-zero values myValues.push_back(it->getValueAt(i)); - } - } + } + } if (myValues.size()==0) { - cerr << "Error: no windows with reads\n"; - cerr << "Unable to proceed..\n"; - exit(-1); + cerr << "Error: no windows with reads\n"; + cerr << "Unable to proceed..\n"; + exit(-1); } - float median = get_median(myValues); - myValues.clear(); - return floor(median); + float median = get_median(myValues); + myValues.clear(); + return floor(median); } double GenomeCopyNumber::calculateMedianAround (float interval, float around) { - float maxCG = around+interval; - float minCG = around-interval; + float maxCG = around+interval; + float minCG = around-interval; - vector myValuesAround; - vector::iterator it; + vector myValuesAround; + vector::iterator it; int countAutosomes = 0; @@ -1040,14 +1043,14 @@ double GenomeCopyNumber::calculateMedianAround (float interval, float around) { } - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (countAutosomes>0 && ! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos) || countAutosomes==0) - for (int i = 0; i< it->getLength(); i++) { - if ((it->getCGprofileAt(i)<=maxCG)&&(it->getCGprofileAt(i)>=minCG)) - if (it->getValueAt(i) >0) //non-zero values - myValuesAround.push_back(it->getValueAt(i)); - } - } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (countAutosomes>0 && ! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos) || countAutosomes==0) + for (int i = 0; i< it->getLength(); i++) { + if ((it->getCGprofileAt(i)<=maxCG)&&(it->getCGprofileAt(i)>=minCG)) + if (it->getValueAt(i) >0) //non-zero values + myValuesAround.push_back(it->getValueAt(i)); + } + } if (myValuesAround.size()==0) { cerr << "Error: zero reads in windows with the GC-content around "< myValuesAround; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - vector controlcounts = controlCopyNumber.getChrCopyNumber(it->getChromosome()).getValues() ; + vector myValuesAround; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { + vector controlcounts = controlCopyNumber.getChrCopyNumber(it->getChromosome()).getValues() ; //check that everything is all right: if (int(controlcounts.size())!=it->getLength()) { cerr << "Possible Error: calculateMedianAround ()\n"; } - for (int i = 0; i< it->getLength(); i++) { - float controlValue = controlcounts[i]; - if ((controlValue<=maxVal)&&(controlValue>=minVal)) - myValuesAround.push_back(it->getValueAt(i)); - } - controlcounts.clear(); + for (int i = 0; i< it->getLength(); i++) { + float controlValue = controlcounts[i]; + if ((controlValue<=maxVal)&&(controlValue>=minVal)) + myValuesAround.push_back(it->getValueAt(i)); + } + controlcounts.clear(); } - } + } if (myValuesAround.size()==0) { cerr << "Warning: zero reads in windows with the Read Count around "<::iterator it; + vector::iterator it; for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { it->removeLowReadCountWindows(controlCopyNumber.getChrCopyNumber(it->getChromosome()), RCThresh); - } + } } void GenomeCopyNumber::removeLowReadCountWindowsFromControl(int RCThresh) { cout << "..will process the control file as well: removing all windows with read count in the control less than "<::iterator it; + vector::iterator it; for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { it->removeLowReadCountWindows(RCThresh); - } + } } int GenomeCopyNumber::getNumberOfChromosomes() { @@ -1135,23 +1138,23 @@ bool GenomeCopyNumber::ifHasRatio() { return 0; } -long double GenomeCopyNumber::calculateRSS(int ploidy) +long double GenomeCopyNumber::calculateRSS(int ploidy) { string::size_type pos = 0; vector observedvalues; vector expectedvalues; - map::iterator it; - for (it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - string chrNumber = (*it).first; - if ( ( pos = chrNumber.find("chr")) != string::npos ) - chrNumber.replace( pos, 3, "" ); + map::iterator it; + for (it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + string chrNumber = (*it).first; + if ( ( pos = chrNumber.find("chr")) != string::npos ) + chrNumber.replace( pos, 3, "" ); if ( ( pos = chrNumber.find("X")) != string::npos ) //exclude X and Y from the analysis continue; if ( ( pos = chrNumber.find("Y")) != string::npos ) continue; - int index = findIndex(chrNumber); - int length = chrCopyNumber_[index].getLength(); - for (int i = 0; i< length; i++) { + int index = findIndex(chrNumber); + int length = chrCopyNumber_[index].getLength(); + for (int i = 0; i< length; i++) { float observed = chrCopyNumber_[index].getRatioAtBin(i); if (observed!=NA) { if (isRatioLogged_) { @@ -1167,39 +1170,39 @@ long double GenomeCopyNumber::calculateRSS(int ploidy) observedvalues.push_back(observed); expectedvalues.push_back(expected); } - } - } + } + } long double RSS = 0; for (int i = 0; i < (int)observedvalues.size(); i++) - { + { if ((observedvalues[i]!=NA) && (expectedvalues[i]!=NA)) - { + { long double diff = (long double)observedvalues[i] - (long double)round(ploidy*expectedvalues[i])/ploidy; RSS = RSS + (long double)pow(diff,2); - } } + } if (observedvalues.size()==0) { return 0; } double normRSS = (RSS/observedvalues.size()); observedvalues.clear();expectedvalues.clear(); - return normRSS; + return normRSS; } void GenomeCopyNumber::calculateRatioUsingCG( GenomeCopyNumber & controlCopyNumber) { //since the raio should be already normalized, just devide sample/control - vector::iterator it; + vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { //should take into account that normally one has only one copy of X and Y.. it->recalculateRatio(controlCopyNumber.getChrCopyNumber(it->getChromosome())); it->recalculateRatio(2); - } else + } else it->recalculateRatio(controlCopyNumber.getChrCopyNumber(it->getChromosome())); - } + } } void GenomeCopyNumber::calculateRatioUsingCG_Regression( GenomeCopyNumber & controlCopyNumber) { @@ -1250,7 +1253,7 @@ void GenomeCopyNumber::calculateRatioUsingCG_Regression( GenomeCopyNumber & cont std::ofstream file; file.open(nametmp); for ( unsigned int i=0 ;irecalculateRatio(controlCopyNumber.getChrCopyNumber(it->getChromosome())); - it->recalculateRatio(a[0]); - } + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->recalculateRatio(controlCopyNumber.getChrCopyNumber(it->getChromosome())); + it->recalculateRatio(a[0]); + } - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { //should take into account that normally one has only one copy of X and Y.. it->recalculateRatio(2); - } - } + } + } - //XXX + //XXX } int GenomeCopyNumber::fillInRatio() { @@ -1287,21 +1290,21 @@ int GenomeCopyNumber::fillInRatio() { for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { if ((sex_.compare("XY")==0) && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - //should take into account that normally one has only one copy of X and Y.. - it->fillInRatio(isRatioLogged_); + //should take into account that normally one has only one copy of X and Y.. + it->fillInRatio(isRatioLogged_); } else { - it->fillInRatio(isRatioLogged_); - for (int i = 0; i< it->getLength(); i++) { - if (it->getValueAt(i)>0) { - countValues.push_back(it->getRatioAtBin(i)); - } + it->fillInRatio(isRatioLogged_); + for (int i = 0; i< it->getLength(); i++) { + if (it->getValueAt(i)>0) { + countValues.push_back(it->getRatioAtBin(i)); } + } } } float median=get_medianNotNA(countValues); for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { if (!isRatioLogged_) { - it->recalculateRatio(median); + it->recalculateRatio(median); } else { it->recalculateLogRatio(median); } @@ -1318,7 +1321,7 @@ int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int int successfulFit = 0; - if(isRatioLogged_) { + if(isRatioLogged_) { intercept=1; degree=1;//because it is loglogscale vector y; //y ~ a0x+a1 vector x; @@ -1344,42 +1347,42 @@ int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int cout << "Initial guess for polynomial:\n"; int nvars = degree; //1 if the fit is linear - ap::real_2d_array xy; - int npoints = x.size(); - xy.setlength(npoints,nvars+1); - int pos = 0; - for (int i = 0; i <(int)x.size(); i++) { - xy(pos,degree) = y[i]; - xy(pos,degree-1) = x[i];; - for (int j = degree-2; j>=0; j--) { - xy(pos,j)=xy(pos,j+1)*x[i]; - } - pos++; - } - linearmodel lm; - int info; - lrreport ar; - if (intercept) - lrbuild(xy,npoints,nvars,info,lm,ar); - else - lrbuildz(xy,npoints,nvars,info,lm,ar); + ap::real_2d_array xy; + int npoints = x.size(); + xy.setlength(npoints,nvars+1); + int pos = 0; + for (int i = 0; i <(int)x.size(); i++) { + xy(pos,degree) = y[i]; + xy(pos,degree-1) = x[i];; + for (int j = degree-2; j>=0; j--) { + xy(pos,j)=xy(pos,j+1)*x[i]; + } + pos++; + } + linearmodel lm; + int info; + lrreport ar; + if (intercept) + lrbuild(xy,npoints,nvars,info,lm,ar); + else + lrbuildz(xy,npoints,nvars,info,lm,ar); if (info != 1) { - cerr << "Error in linear regression, code: " << info <<"\n"; - } - ap::real_1d_array v; - v.setlength(nvars+1); - lrunpack(lm,v,nvars); - double a[MAXDEGREE+1]; + cerr << "Error in linear regression, code: " << info <<"\n"; + } + ap::real_1d_array v; + v.setlength(nvars+1); + lrunpack(lm,v,nvars); + double a[MAXDEGREE+1]; - for (int i = 0; i 1) { @@ -1400,7 +1403,7 @@ int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int successfulFit = 1; } - if (degree == 1) { + if (degree == 1) { cout << "log(Y) = " << a[0] << "*log(x)+" << a[1] << "\n"; } if (degree > 1) { @@ -1422,7 +1425,7 @@ int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int } - } else { + } else { if (WESanalysis == true){ degree = 1; @@ -1438,10 +1441,10 @@ int GenomeCopyNumber::calculateRatio( GenomeCopyNumber & controlCopyNumber, int double around [MAXDEGREE+2] ; - int lquar, uquar; - controlCopyNumber.calculateReadCountQuartiles(lquar, uquar); - double minVal = lquar; - double maxVal = uquar; + int lquar, uquar; + controlCopyNumber.calculateReadCountQuartiles(lquar, uquar); + double minVal = lquar; + double maxVal = uquar; for (int i = 0; i myValues; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) - for (int i = 0; i< it->getLength(); i++) { - if (it->getValueAt(i) >0) //non-zero values - myValues.push_back(it->getValueAt(i)); - } - } + vector myValues; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) + for (int i = 0; i< it->getLength(); i++) { + if (it->getValueAt(i) >0) //non-zero values + myValues.push_back(it->getValueAt(i)); + } + } - if (myValues.size()==0) { - cerr << "Error: no windows with reads\n"; - cerr << "Unable to proceed..\n"; - exit(-1); - } + if (myValues.size()==0) { + cerr << "Error: no windows with reads\n"; + cerr << "Unable to proceed..\n"; + exit(-1); + } - sort(myValues.begin(), myValues.end()); - lower = myValues[myValues.size() / 4]; - upper = myValues[(3 * myValues.size()) / 4]; + sort(myValues.begin(), myValues.end()); + lower = myValues[myValues.size() / 4]; + upper = myValues[(3 * myValues.size()) / 4]; } float GenomeCopyNumber::getMedianRatio() { - vectorselectedValues; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - vector chr_values = it->getRatio(); - for (int i = 0; i<(int)chr_values.size(); i++) - if (chr_values[i]!=NA) - selectedValues.push_back(chr_values[i]); - else - cout << chr_values[i] <<"\n"; - } - float median = get_median(selectedValues); - selectedValues.clear(); - return median; + vectorselectedValues; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + vector chr_values = it->getRatio(); + for (int i = 0; i<(int)chr_values.size(); i++) + if (chr_values[i]!=NA) + selectedValues.push_back(chr_values[i]); + else + cout << chr_values[i] <<"\n"; + } + float median = get_median(selectedValues); + selectedValues.clear(); + return median; } float GenomeCopyNumber::calculateNormalizationConstant(GenomeCopyNumber & controlCopyNumber) { - float median,medianControl; - median = getMedianCopyNumber(); - medianControl = controlCopyNumber.getMedianCopyNumber(); - return median/medianControl;; + float median,medianControl; + median = getMedianCopyNumber(); + medianControl = controlCopyNumber.getMedianCopyNumber(); + return median/medianControl;; } float GenomeCopyNumber::getMedianCopyNumber() { - vectorselectedValues; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - vector chr_values = it->getValues(); - for (int i = 0; i<(int)chr_values.size(); i++) - //if (chr_values[i]!=0) - selectedValues.push_back(chr_values[i]); - } - float median = get_median(selectedValues); - //float mean = get_mean(selectedValues); - selectedValues.clear(); + vectorselectedValues; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + vector chr_values = it->getValues(); + for (int i = 0; i<(int)chr_values.size(); i++) + //if (chr_values[i]!=0) + selectedValues.push_back(chr_values[i]); + } + float median = get_median(selectedValues); + //float mean = get_mean(selectedValues); + selectedValues.clear(); return median; } ChrCopyNumber GenomeCopyNumber::getChrCopyNumber(std::string const& chr) { - int index = findIndex(chr); - if (index==NA) throw "No such chromosome"; - return chrCopyNumber_[index]; + int index = findIndex(chr); + if (index==NA) throw "No such chromosome"; + return chrCopyNumber_[index]; } -void GenomeCopyNumber::printRatio(std::string const& outFile, bool ifBedGraphOutPut, bool printNA) { +void GenomeCopyNumber::printRatio(std::string const& outFile, bool ifBedGraphOutPut, bool printNA, bool has_smoothed_profile /*= false*/, bool has_MAF /*= false*/) { std::ofstream file (outFile.c_str()); map::iterator it; if (ifBedGraphOutPut==false) { file << "Chromosome\tStart\tRatio\tMedianRatio\tCopyNumber"; + if (has_smoothed_profile == true) { + file << "\tSmoothedRatio\tRescaledRatio"; + } + if (hasBAF_==1){ file << "\tBAF\testimatedBAF\tGenotype\tUncertaintyOfGT"; } + if (has_MAF == true) { + file << "\tSampledBAF\tSampledMAF\tSmoothedMAF"; + } if (WESanalysis == true) - { + { file << "\tGene"; - } + } if (SeekingSubc_ == true) - { + { file << "\tSubclone_CN\tSubclone_Population"; - } + } file << "\n"; for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - printRatio((*it).first,file,printNA); + printRatio((*it).first,file,printNA, has_smoothed_profile, has_MAF); } } else { @@ -1718,76 +1728,76 @@ void GenomeCopyNumber::printRatio(std::string const& outFile, bool ifBedGraphOut void GenomeCopyNumber::printBAF(std::string const& outFile, SNPinGenome& snpingenome, std::string const& matefile) { string myName = outFile; string outfile = myName + "_BAF.txt"; - std::ofstream file (outfile.c_str()); - map::iterator it; - file << "Chromosome\tPosition\tBAF\tFittedA\tFittedB\tA\tB\tuncertainty"; - file << "\n"; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + std::ofstream file (outfile.c_str()); + map::iterator it; + file << "Chromosome\tPosition\tBAF\tFittedA\tFittedB\tA\tB\tuncertainty"; + file << "\n"; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - string chrNumber = (*it).first; + string chrNumber = (*it).first; int indexSNP = snpingenome.findIndex(chrNumber); if (indexSNP == NA) { - cerr << "An error occurred in GenomeCopyNumber::printBAF: could not find an SNP index for "<::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - it->deleteFlanks(telo_centromeric_flanks); - } + telo_centromeric_flanks_ = telo_centromeric_flanks; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->deleteFlanks(telo_centromeric_flanks); + } } void GenomeCopyNumber::recalcFlanks(int telo_centromeric_flanks, int minNumberOfWindows) { - telo_centromeric_flanks_ = telo_centromeric_flanks; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - it->recalcFlanks(telo_centromeric_flanks, minNumberOfWindows); - } + telo_centromeric_flanks_ = telo_centromeric_flanks; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->recalcFlanks(telo_centromeric_flanks, minNumberOfWindows); + } } void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointType) - { - //estimationOfExomeSize_ = 0; - vector::iterator it; - unsigned long long count = 0; +{ + //estimationOfExomeSize_ = 0; + vector::iterator it; + unsigned long long count = 0; int endsSize=0; - string NormalBAF,NormalBAF_XY; + string NormalBAF,NormalBAF_XY; float normalXYploidy=ploidy_*0.5; //will only use it when the genome is male estimationOfGenomeSize_=0; if (hasBAF_) - { - NormalBAF = getNormalBAFforPloidy(ploidy_); - NormalBAF_XY=getXYBAFforPloidy(ploidy_);//will only use it when the genome is male - } + { + NormalBAF = getNormalBAFforPloidy(ploidy_); + NormalBAF_XY=getXYBAFforPloidy(ploidy_);//will only use it when the genome is male + } CNVs_.clear(); copyNumberProbs_.clear(); - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) - { - float previousLevel = NA; - int lengthOfPreviousLevel = 0; - float nextLevel = NA; - int lengthOfNextLevel = 0; - it->setIsSmoothed(true); - string chr = it->getChromosome(); - cout << "..Annotation of CNVs for "<< chr <<"\n"; - //will use these three variables to collect CNVs: - int start = 0; - int end = NA; - int cnumber = NA; - string BAFSym = "-"; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) + { + float previousLevel = NA; + int lengthOfPreviousLevel = 0; + float nextLevel = NA; + int lengthOfNextLevel = 0; + it->setIsSmoothed(true); + string chr = it->getChromosome(); + cout << "..Annotation of CNVs for "<< chr <<"\n"; + //will use these three variables to collect CNVs: + int start = 0; + int end = NA; + int cnumber = NA; + string BAFSym = "-"; string BAFprev = "-"; string BAFnext = "-"; string lBAF = "-"; @@ -1799,31 +1809,31 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { normalLevel = 0.5; } - for (int i = 0; i<(int)it->getMedianValues().size(); i++) { - float level = it->getLevelAt(i, ploidy_); - int fragmentLength = it->getFragmentLengths()[i]; + for (int i = 0; i<(int)it->getMedianValues().size(); i++) { + float level = it->getLevelAt(i, ploidy_); + int fragmentLength = it->getFragmentLengths()[i]; if (hasBAF_) { BAFSym = it->getBAFsymbPerFrg(i); BAFUncertainty = it->getEstimatedBAFuncertaintyAtBin(i); // cout << "..Control: read "<< BAFSym << "\n"; } - if (level == NA) - { - int nextIndex = it->nextNoNAIndex(i, ploidy_,0); - BAFUncertainty = NA; - if (nextIndex == NA) { - nextLevel = NA; - lengthOfNextLevel = 0; - BAFnext = "-"; - } else { - nextLevel = it->getLevelAt(nextIndex, ploidy_); - lengthOfNextLevel = it->getFragmentLengthsAt(nextIndex); + if (level == NA) + { + int nextIndex = it->nextNoNAIndex(i, ploidy_,0); + BAFUncertainty = NA; + if (nextIndex == NA) { + nextLevel = NA; + lengthOfNextLevel = 0; + BAFnext = "-"; + } else { + nextLevel = it->getLevelAt(nextIndex, ploidy_); + lengthOfNextLevel = it->getFragmentLengthsAt(nextIndex); if (hasBAF_) BAFnext = it->getBAFsymbPerFrg(nextIndex); - } - //nextLevel = round_by_ploidy(it->nextNoNAMedian(i, ploidy_), ploidy_); - //lengthOfNextLevel = it->nextNoNALength(i, ploidy_); + } + //nextLevel = round_by_ploidy(it->nextNoNAMedian(i, ploidy_), ploidy_); + //lengthOfNextLevel = it->nextNoNALength(i, ploidy_); if (breakPointType==NOCALL) { if ((previousLevel != NA) && (nextLevel != NA) && previousLevel==nextLevel && previousLevel==normalLevel) { @@ -1849,15 +1859,15 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy //if (nextLevel == 1) // level = 1; } else - if (nextLevel == NA) { - level = previousLevel; - if (hasBAF_) - BAFSym = BAFprev; - } else { - level = nextLevel; - if (hasBAF_) - BAFSym = BAFnext; - } + if (nextLevel == NA) { + level = previousLevel; + if (hasBAF_) + BAFSym = BAFprev; + } else { + level = nextLevel; + if (hasBAF_) + BAFSym = BAFnext; + } } else if (breakPointType==NORMALLEVEL) { if ((previousLevel == normalLevel) || (nextLevel == normalLevel) ) { level = normalLevel; @@ -1878,46 +1888,46 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy BAFSym = BAFnext; } } else - if (nextLevel == NA) { - level = previousLevel; - if (hasBAF_) - BAFSym = BAFprev; - } else { - level = nextLevel; - if (hasBAF_) - BAFSym = BAFnext; - } + if (nextLevel == NA) { + level = previousLevel; + if (hasBAF_) + BAFSym = BAFprev; + } else { + level = nextLevel; + if (hasBAF_) + BAFSym = BAFnext; + } } } if (level == NA) level = normalLevel; //should never happen } - } - int copyNumber = round_f(level*ploidy_); - //if (copyNumber < 0) //should happen only with "NOCALL" - // copyNumber = NA; - if (copyNumberProbs_.count(copyNumber) == 0) { - copyNumberProbs_.insert ( pair(copyNumber,0) ); - } - if (it->getEndsSize()==0) { - copyNumberProbs_.find(copyNumber)->second += fragmentLength; - if (copyNumber > NA) { + } + int copyNumber = round_f(level*ploidy_); + //if (copyNumber < 0) //should happen only with "NOCALL" + // copyNumber = NA; + if (copyNumberProbs_.count(copyNumber) == 0) { + copyNumberProbs_.insert ( pair(copyNumber,0) ); + } + if (it->getEndsSize()==0) { + copyNumberProbs_.find(copyNumber)->second += fragmentLength; + if (copyNumber > NA) { estimationOfGenomeSize_ += copyNumber*fragmentLength; count+=fragmentLength; - } + } - if (cnumber == NA) { - end = fragmentLength-1; - cnumber = round_f(level*ploidy_); - lBAF = BAFSym; + if (cnumber == NA) { + end = fragmentLength-1; + cnumber = round_f(level*ploidy_); + lBAF = BAFSym; lUncertainty = BAFUncertainty ; //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { - int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size - if (realEndOfTheCNV > it->getChrLength()) + } else { + if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { + int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size + if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); if (hasBAF_ && lBAF!="" && lBAF.compare("-")!=0) @@ -1930,10 +1940,10 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF_XY)!=0 && cnumber == normalXYploidy && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } else { + } else { if (cnumber != ploidy_ && cnumber != NA) //push previous entry if (hasBAF_) @@ -1941,44 +1951,44 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF)!=0 && cnumber == ploidy_ && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + } - //fill corresponding smoothed profile: + //fill corresponding smoothed profile: - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - start = end+1; - end = start+fragmentLength-1; - cnumber = round_f(level*ploidy_); + start = end+1; + end = start+fragmentLength-1; + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - end = end+fragmentLength; //should almost never happen if (hasBAF_) - } - } - } else { - if (cnumber == NA) { - end = fragmentLength-1; //should only once, in the beginning - cnumber = round_f(level*ploidy_); + } else { + end = end+fragmentLength; //should almost never happen if (hasBAF_) + } + } + } else { + if (cnumber == NA) { + end = fragmentLength-1; //should only once, in the beginning + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; - //if (cnumber < 0) //should happen only with "NOCALL" + //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { //save previous value: - int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; - copyNumberProbs_.find(cnumber)->second += realLength; - if (cnumber>=0) { + } else { + if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { //save previous value: + int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; + copyNumberProbs_.find(cnumber)->second += realLength; + if (cnumber>=0) { estimationOfGenomeSize_ += cnumber*realLength; count+=realLength; } int realEndOfTheCNV=it->getEndAtBin(end); //check that CNV is not larger than chr size - if (realEndOfTheCNV > it->getChrLength()) + if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); @@ -1988,16 +1998,16 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - if (cnumber != normalXYploidy && cnumber >= 0) //push previous entry + if (cnumber != normalXYploidy && cnumber >= 0) //push previous entry if (hasBAF_) CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF_XY)!=0 && cnumber == normalXYploidy && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } else { + } else { if (cnumber != ploidy_ && cnumber >= 0) //push previous entry if (hasBAF_) @@ -2005,35 +2015,35 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF)!=0 && cnumber == ploidy_ && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV } - //fill corresponding smoothed profile: - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + //fill corresponding smoothed profile: + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - start = end+1; - end = start+fragmentLength-1; - cnumber = round_f(level*ploidy_); + start = end+1; + end = start+fragmentLength-1; + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; - //if (cnumber < 0) //should happen only with "NOCALL" + //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - end = end+fragmentLength; - } - } + } else { + end = end+fragmentLength; + } + } - } - } - //save the last CNV for this chromosomerealLength + } + } + //save the last CNV for this chromosomerealLength if (hasBAF_ && lBAF!="" && lBAF.compare("-")!=0) cnumber = lBAF.length(); - if (it->getEndsSize()==0) { + if (it->getEndsSize()==0) { int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); @@ -2063,19 +2073,19 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy } - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); - } else { - endsSize = it->getEndsSize(); - int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; - copyNumberProbs_.find(cnumber)->second += realLength; - if (cnumber>0) { + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); + } else { + endsSize = it->getEndsSize(); + int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; + copyNumberProbs_.find(cnumber)->second += realLength; + if (cnumber>0) { estimationOfGenomeSize_ += cnumber*realLength; count+=realLength; } int realEndOfTheCNV=it->getEndAtBin(end); //check that CNV is not larger than chr size if (realEndOfTheCNV > it->getChrLength()) - realEndOfTheCNV=it->getChrLength(); + realEndOfTheCNV=it->getChrLength(); if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { @@ -2099,39 +2109,39 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_exomeLength(int breakPointTy } - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - } + } - } - if (endsSize==0) { - estimationOfGenomeSize_ *= windowSize_; - } else { - //do nothing - } - map::iterator it2; - for ( it2=copyNumberProbs_.begin() ; it2 != copyNumberProbs_.end(); it2++ ) { - if ((*it2).first>0) { + } + if (endsSize==0) { + estimationOfGenomeSize_ *= windowSize_; + } else { + //do nothing + } + map::iterator it2; + for ( it2=copyNumberProbs_.begin() ; it2 != copyNumberProbs_.end(); it2++ ) { + if ((*it2).first>0) { cout << (*it2).first << "\t"<< (*it2).second/count<< "\n"; - } + } - } + } } void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointType) { - estimationOfGenomeSize_ = 0; + estimationOfGenomeSize_ = 0; - vector::iterator it; - unsigned long long count = 0; + vector::iterator it; + unsigned long long count = 0; int min_fragment= telo_centromeric_flanks_/step_; - int endsSize=0; - string NormalBAF,NormalBAF_XY; + int endsSize=0; + string NormalBAF,NormalBAF_XY; float normalXYploidy=ploidy_*0.5; //will only use it when the genome is male if (hasBAF_) { - NormalBAF = getNormalBAFforPloidy(ploidy_); - NormalBAF_XY=getXYBAFforPloidy(ploidy_);//will only use it when the genome is male + NormalBAF = getNormalBAFforPloidy(ploidy_); + NormalBAF_XY=getXYBAFforPloidy(ploidy_);//will only use it when the genome is male } CNVs_.clear(); @@ -2141,21 +2151,21 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT cout << "copyNumberProbs_ contains:\n"; map::iterator itProb; for ( itProb=copyNumberProbs_.begin() ; itProb != copyNumberProbs_.end(); itProb++ ) - cout << (*itProb).first << " => " << (*itProb).second << "\n"; - - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - float previousLevel = NA; - int lengthOfPreviousLevel = 0; - float nextLevel = NA; - int lengthOfNextLevel = 0; - it->setIsSmoothed(true); - string chr = it->getChromosome(); - cout << "..Annotation of CNVs for "<< chr <<"\n"; - //will use these three variables to collect CNVs: - int start = 0; - int end = NA; - int cnumber = NA; - string BAFSym = "-"; + cout << (*itProb).first << " => " << (*itProb).second << "\n"; + + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + float previousLevel = NA; + int lengthOfPreviousLevel = 0; + float nextLevel = NA; + int lengthOfNextLevel = 0; + it->setIsSmoothed(true); + string chr = it->getChromosome(); + cout << "..Annotation of CNVs for "<< chr <<"\n"; + //will use these three variables to collect CNVs: + int start = 0; + int end = NA; + int cnumber = NA; + string BAFSym = "-"; string BAFprev = "-"; string BAFnext = "-"; string lBAF = "-"; @@ -2168,42 +2178,42 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT normalLevel = 0.5; } - for (int i = 0; i<(int)it->getMedianValues().size(); i++) { - float level = it->getLevelAt(i, ploidy_); - int fragmentLength = it->getFragmentLengths()[i]; + for (int i = 0; i<(int)it->getMedianValues().size(); i++) { + float level = it->getLevelAt(i, ploidy_); + int fragmentLength = it->getFragmentLengths()[i]; if (hasBAF_) { BAFSym = it->getBAFsymbPerFrg(i); BAFUncertainty = it->getEstimatedBAFuncertaintyAtBin(i); // cout << "..Control: read "<< BAFSym << "\n"; } - if (breakPointType==HALFLENGTH && i<(int)it->getMedianValues().size()-1) { + if (breakPointType==HALFLENGTH && i<(int)it->getMedianValues().size()-1) { min_fragment = (it->getFragmentLengths()[i+1]+1)/2; - } - if (level != NA) { - if (fragmentLength>min_fragment) { - previousLevel = level; - lengthOfPreviousLevel = fragmentLength; - BAFprev = BAFSym; - } - } else { + } + if (level != NA) { + if (fragmentLength>min_fragment) { + previousLevel = level; + lengthOfPreviousLevel = fragmentLength; + BAFprev = BAFSym; + } + } else { if (breakPointType==HALFLENGTH) { min_fragment = (it->getFragmentLengths()[i]+1)/2; } - int nextIndex = it->nextNoNAIndex(i, ploidy_,min_fragment); - BAFUncertainty = NA; - if (nextIndex == NA) { - nextLevel = NA; - lengthOfNextLevel = 0; - BAFnext = "-"; - } else { - nextLevel = it->getLevelAt(nextIndex, ploidy_); - lengthOfNextLevel = it->getFragmentLengthsAt(nextIndex); + int nextIndex = it->nextNoNAIndex(i, ploidy_,min_fragment); + BAFUncertainty = NA; + if (nextIndex == NA) { + nextLevel = NA; + lengthOfNextLevel = 0; + BAFnext = "-"; + } else { + nextLevel = it->getLevelAt(nextIndex, ploidy_); + lengthOfNextLevel = it->getFragmentLengthsAt(nextIndex); if (hasBAF_) BAFnext = it->getBAFsymbPerFrg(nextIndex); - } - //nextLevel = round_by_ploidy(it->nextNoNAMedian(i, ploidy_), ploidy_); - //lengthOfNextLevel = it->nextNoNALength(i, ploidy_); + } + //nextLevel = round_by_ploidy(it->nextNoNAMedian(i, ploidy_), ploidy_); + //lengthOfNextLevel = it->nextNoNALength(i, ploidy_); if (breakPointType==NOCALL) { if ((previousLevel != NA) && (nextLevel != NA) && previousLevel==nextLevel && previousLevel==normalLevel) { @@ -2229,15 +2239,15 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT //if (nextLevel == 1) // level = 1; } else - if (nextLevel == NA) { - level = previousLevel; - if (hasBAF_) - BAFSym = BAFprev; - } else { - level = nextLevel; - if (hasBAF_) - BAFSym = BAFnext; - } + if (nextLevel == NA) { + level = previousLevel; + if (hasBAF_) + BAFSym = BAFprev; + } else { + level = nextLevel; + if (hasBAF_) + BAFSym = BAFnext; + } } else if (breakPointType==NORMALLEVEL) { if ((previousLevel == normalLevel) || (nextLevel == normalLevel) ) { level = normalLevel; @@ -2258,46 +2268,46 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT BAFSym = BAFnext; } } else - if (nextLevel == NA) { - level = previousLevel; - if (hasBAF_) - BAFSym = BAFprev; - } else { - level = nextLevel; - if (hasBAF_) - BAFSym = BAFnext; - } + if (nextLevel == NA) { + level = previousLevel; + if (hasBAF_) + BAFSym = BAFprev; + } else { + level = nextLevel; + if (hasBAF_) + BAFSym = BAFnext; + } } } if (level == NA) level = normalLevel; //should never happen } - } - int copyNumber = round_f(level*ploidy_); - //if (copyNumber < 0) //should happen only with "NOCALL" + } + int copyNumber = round_f(level*ploidy_); + //if (copyNumber < 0) //should happen only with "NOCALL" // copyNumber = NA; - if (copyNumberProbs_.count(copyNumber) == 0) { - copyNumberProbs_.insert ( pair(copyNumber,0) ); - } - if (it->getEndsSize()==0) { - copyNumberProbs_.find(copyNumber)->second += fragmentLength; - if (copyNumber > NA) { + if (copyNumberProbs_.count(copyNumber) == 0) { + copyNumberProbs_.insert ( pair(copyNumber,0) ); + } + if (it->getEndsSize()==0) { + copyNumberProbs_.find(copyNumber)->second += fragmentLength; + if (copyNumber > NA) { estimationOfGenomeSize_ += copyNumber*fragmentLength; count+=fragmentLength; - } + } - if (cnumber == NA) { - end = fragmentLength-1; - cnumber = round_f(level*ploidy_); - lBAF = BAFSym; + if (cnumber == NA) { + end = fragmentLength-1; + cnumber = round_f(level*ploidy_); + lBAF = BAFSym; lUncertainty = BAFUncertainty ; //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { - int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size - if (realEndOfTheCNV > it->getChrLength()) + } else { + if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { + int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size + if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); if (hasBAF_ && lBAF!="" && lBAF.compare("-")!=0) @@ -2310,10 +2320,10 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF_XY)!=0 && cnumber == normalXYploidy && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } else { + } else { if (cnumber != ploidy_ && cnumber != NA) //push previous entry if (hasBAF_) @@ -2321,44 +2331,44 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF)!=0 && cnumber == ploidy_ && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + } - //fill corresponding smoothed profile: + //fill corresponding smoothed profile: - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - start = end+1; - end = start+fragmentLength-1; - cnumber = round_f(level*ploidy_); + start = end+1; + end = start+fragmentLength-1; + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - end = end+fragmentLength; //should almost never happen if (hasBAF_) - } - } - } else { - if (cnumber == NA) { - end = fragmentLength-1; //should only once, in the beginning - cnumber = round_f(level*ploidy_); + } else { + end = end+fragmentLength; //should almost never happen if (hasBAF_) + } + } + } else { + if (cnumber == NA) { + end = fragmentLength-1; //should only once, in the beginning + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; - //if (cnumber < 0) //should happen only with "NOCALL" + //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { //save previous value: - int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; - copyNumberProbs_.find(cnumber)->second += realLength; - if (cnumber>=0) { + } else { + if (round_f(level*ploidy_) != cnumber || lBAF.compare(BAFSym)!=0 || lUncertainty != BAFUncertainty) { //save previous value: + int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; + copyNumberProbs_.find(cnumber)->second += realLength; + if (cnumber>=0) { estimationOfGenomeSize_ += cnumber*realLength; count+=realLength; } int realEndOfTheCNV=it->getEndAtBin(end); //check that CNV is not larger than chr size - if (realEndOfTheCNV > it->getChrLength()) + if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); @@ -2368,16 +2378,16 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - if (cnumber != normalXYploidy && cnumber >= 0) //push previous entry + if (cnumber != normalXYploidy && cnumber >= 0) //push previous entry if (hasBAF_) CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF_XY)!=0 && cnumber == normalXYploidy && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV - } else { + } else { if (cnumber != ploidy_ && cnumber >= 0) //push previous entry if (hasBAF_) @@ -2385,35 +2395,35 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT else CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber)); //save previous CNV else if (hasBAF_ && lBAF.compare(NormalBAF)!=0 && cnumber == ploidy_ && lBAF!=""&& lBAF.compare("-")!=0) //abnormal BAF - CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV + CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,it->getCoordinateAtBin(start),realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV } - //fill corresponding smoothed profile: - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + //fill corresponding smoothed profile: + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - start = end+1; - end = start+fragmentLength-1; - cnumber = round_f(level*ploidy_); + start = end+1; + end = start+fragmentLength-1; + cnumber = round_f(level*ploidy_); lBAF = BAFSym; lUncertainty = BAFUncertainty ; - //if (cnumber < 0) //should happen only with "NOCALL" + //if (cnumber < 0) //should happen only with "NOCALL" // cnumber = NA; - } else { - end = end+fragmentLength; - } - } + } else { + end = end+fragmentLength; + } + } - } - } - //save the last CNV for this chromosomerealLength + } + } + //save the last CNV for this chromosomerealLength if (hasBAF_ && lBAF!="" && lBAF.compare("-")!=0) cnumber = lBAF.length(); - if (it->getEndsSize()==0) { + if (it->getEndsSize()==0) { int realEndOfTheCNV=(end+1)*windowSize_; //check that CNV is not larger than chr size if (realEndOfTheCNV > it->getChrLength()) realEndOfTheCNV=it->getChrLength(); @@ -2440,19 +2450,19 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT } - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); - } else { - endsSize = it->getEndsSize(); - int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; - copyNumberProbs_.find(cnumber)->second += realLength; - if (cnumber>0) { + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); + } else { + endsSize = it->getEndsSize(); + int realLength = it->getEndAtBin(end)-it->getCoordinateAtBin(start)+1; + copyNumberProbs_.find(cnumber)->second += realLength; + if (cnumber>0) { estimationOfGenomeSize_ += cnumber*realLength; count+=realLength; } int realEndOfTheCNV=it->getEndAtBin(end); //check that CNV is not larger than chr size if (realEndOfTheCNV > it->getChrLength()) - realEndOfTheCNV=it->getChrLength(); + realEndOfTheCNV=it->getChrLength(); if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { @@ -2476,30 +2486,30 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT } - for (int j = start; j<= end; j++) - it->pushSmoothedProfile(float(cnumber)/ploidy_); + for (int j = start; j<= end; j++) + it->pushSmoothedProfile(float(cnumber)/ploidy_); - } + } - } - if (endsSize==0) { - estimationOfGenomeSize_ *= windowSize_; - } else { - //do nothing - } - map::iterator it2; - for ( it2=copyNumberProbs_.begin() ; it2 != copyNumberProbs_.end(); it2++ ) { - if ((*it2).first>0) { + } + if (endsSize==0) { + estimationOfGenomeSize_ *= windowSize_; + } else { + //do nothing + } + map::iterator it2; + for ( it2=copyNumberProbs_.begin() ; it2 != copyNumberProbs_.end(); it2++ ) { + if ((*it2).first>0) { cout << (*it2).first << "\t"<< (*it2).second/count<< "\n"; - } + } - } + } } void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) { - ifstream file (inFile.c_str()); - string line; + ifstream file (inFile.c_str()); + string line; string::size_type pos = 0; string currentChr = ""; int index = NA; @@ -2512,17 +2522,17 @@ void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) { int endPos = 0; int lastEnd = -1; string text = ""; - if (file.is_open()) { - cout << "..Reading "<< inFile << "\n"; - int countChromosomes = 0; - int countChromosomesOutOfIndex = 0; - isMappUsed_=true; - while (! file.eof() ) { - getline (file,line); - if (! line.length()) continue; - pos = 0; - if ( (line.substr(0,1) == "~") && (line.substr(0,2) != "~~")){ - //if ( ( pos = line.find("~chr", pos)) != string::npos ){ + if (file.is_open()) { + cout << "..Reading "<< inFile << "\n"; + int countChromosomes = 0; + int countChromosomesOutOfIndex = 0; + isMappUsed_=true; + while (! file.eof() ) { + getline (file,line); + if (! line.length()) continue; + pos = 0; + if ( (line.substr(0,1) == "~") && (line.substr(0,2) != "~~")){ + //if ( ( pos = line.find("~chr", pos)) != string::npos ){ //save the last info: if (count > endPos && index != NA) { // endPos ? int howMuchToDelete = startPos-lastEnd-1; @@ -2545,19 +2555,19 @@ void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) { index = findIndex(currentChr); positionInd = 0; - count = 0; - uniqueCount = 0; + count = 0; + uniqueCount = 0; text = ""; lastEnd = -1; //cout << "..Index for chromosome " << currentChr << ": "<< index << "\n"; - if (index == NA) { - cout << "skipping chromosome " << currentChr << "\n"; - countChromosomesOutOfIndex ++; - //return; - // do not return! they can be other "good" chromosomes afterwords! - //do nothing!!! wait for the next chromosome! + if (index == NA) { + cout << "skipping chromosome " << currentChr << "\n"; + countChromosomesOutOfIndex ++; + //return; + // do not return! they can be other "good" chromosomes afterwords! + //do nothing!!! wait for the next chromosome! } else { countChromosomes++; @@ -2569,7 +2579,7 @@ void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) { chrCopyNumber_[index].createMappabilityProfile(); } - } else if (index != NA) { + } else if (index != NA) { count += line.length(); text.append(line); @@ -2614,53 +2624,53 @@ void GenomeCopyNumber::readGemMappabilityFile(std::string const& inFile) { index = NA; } } - } - } - file.close(); - //save the very last info (int text variable) + } + } + file.close(); + //save the very last info (int text variable) if (count >= startPos && index != NA) { //endPos uniqueCount =0; - for(int i = 0; i < (int)text.length(); ++i) - if (text[i] == '!') - uniqueCount++; + for(int i = 0; i < (int)text.length(); ++i) + if (text[i] == '!') + uniqueCount++; ratio = float(uniqueCount)/localWindowSize; // /max((int)text.length(),(int)localWindowSize); chrCopyNumber_[index].setMappabilityProfileAt(positionInd, ratio); } - cout << "..file " << inFile << " is read\n"; - cout << "..Mappability profile was taken into account for "<< countChromosomes <<" chromosomes\n"; - cout << ".."<< countChromosomesOutOfIndex <<" chromosomes were skipped\n"; + cout << "..file " << inFile << " is read\n"; + cout << "..Mappability profile was taken into account for "<< countChromosomes <<" chromosomes\n"; + cout << ".."<< countChromosomesOutOfIndex <<" chromosomes were skipped\n"; // if (chrCopyNumber_[1].getLength() == chrCopyNumber_[1].getMappabilityLength()) // cout << "Mappability profile has been set correctly"; - } else{ + } else{ cerr << "Error: Unable to open file "+inFile+"\n"; exit(-1); - } + } } int GenomeCopyNumber::readCGprofile(std::string const& inFile) { - ifstream file (inFile.c_str()); - string line; - int count = 0; - int observedStep = 0; - if (file.is_open()) { - while (! file.eof() ) { - getline (file,line); - if (! line.length()) continue; - std::vector strs = split(line, '\t'); - if (strs.size()>=4) { - string currentChr = strs[0]; - if (observedStep==0) + ifstream file (inFile.c_str()); + string line; + int count = 0; + int observedStep = 0; + if (file.is_open()) { + while (! file.eof() ) { + getline (file,line); + if (! line.length()) continue; + std::vector strs = split(line, '\t'); + if (strs.size()>=4) { + string currentChr = strs[0]; + if (observedStep==0) observedStep = ceil(strtod(strs[1].c_str(), NULL)); - float CGperc =(float)strtod(strs[2].c_str(), NULL); - float nonNperc =(float)strtod(strs[3].c_str(), NULL); - string::size_type pos = 0; - if ( ( pos = currentChr.find("chr", pos)) != string::npos ) - currentChr.replace( pos, 3, "" ); - int index = findIndex(currentChr); - if (index != NA) { - chrCopyNumber_[index].addToCGcontent(CGperc); + float CGperc =(float)strtod(strs[2].c_str(), NULL); + float nonNperc =(float)strtod(strs[3].c_str(), NULL); + string::size_type pos = 0; + if ( ( pos = currentChr.find("chr", pos)) != string::npos ) + currentChr.replace( pos, 3, "" ); + int index = findIndex(currentChr); + if (index != NA) { + chrCopyNumber_[index].addToCGcontent(CGperc); chrCopyNumber_[index].addToNonNpercent(nonNperc); count++; if (strs.size()==5) { //means that there are also mappability values in the 5th colomn @@ -2675,241 +2685,241 @@ int GenomeCopyNumber::readCGprofile(std::string const& inFile) { return observedStep; } - } - } + } + } - strs.clear(); - } - file.close(); - cout << "file " << inFile << " is read\n"; - if (count==0){ + strs.clear(); + } + file.close(); + cout << "file " << inFile << " is read\n"; + if (count==0){ cerr << "Your GC-content file "< strs = split(line, '\t'); - if (strs.size()==3) { - if (strs[0].compare(currentChr)!=0) { - chrCount ++; - currentChr = strs[0]; - chromosomesInd_.insert(pair (currentChr,chrCount)); - chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); - windowSize_ = atoi(strs[1].c_str()); - } - float cp = (float)strtod(strs[2].c_str(), NULL); - chrCopyNumber_[chrCount].addToReadCount(cp); - chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); - normalNumberOfPairs_ += (int)cp; - if (windowSize_ == 0) - windowSize_ = atoi(strs[1].c_str()); - count++; - } - else if (strs.size()==4) { - string chrNumber = strs[0]; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - - if (chrNumber.compare(currentChr)!=0) { - chrCount ++; - currentChr = chrNumber; - chromosomesInd_.insert(pair (currentChr,chrCount)); - chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); - windowSize_ = atoi(strs[2].c_str())-atoi(strs[1].c_str())+1; - } - float cp = (float)strtod(strs[3].c_str(), NULL); - chrCopyNumber_[chrCount].addToReadCount(cp); - chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); - chrCopyNumber_[chrCount].addToEnds(atoi(strs[2].c_str())); - normalNumberOfPairs_ += (int)cp; - if (count>0 && step_==NA) { - // int first = chrCopyNumber_[chrCount].getCoordinateAtBin(0); - // int second = chrCopyNumber_[chrCount].getCoordinateAtBin(1); - step_ = chrCopyNumber_[chrCount].getCoordinateAtBin(1)-chrCopyNumber_[chrCount].getCoordinateAtBin(0); - } + totalNumberOfPairs_ = 0; + normalNumberOfPairs_ = 0; + windowSize_ = 0; + ifstream file (inFile.c_str()); + string line; + string currentChr = ""; + int chrCount = -1; + refGenomeSize_ = 0; + string::size_type pos = 0; + int count = 0; + if (file.is_open()) { + while (! file.eof() ) { + getline (file,line); + + if (! line.length()) continue; + + std::vector strs = split(line, '\t'); + if (strs.size()==3) { + if (strs[0].compare(currentChr)!=0) { + chrCount ++; + currentChr = strs[0]; + chromosomesInd_.insert(pair (currentChr,chrCount)); + chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); + windowSize_ = atoi(strs[1].c_str()); + } + float cp = (float)strtod(strs[2].c_str(), NULL); + chrCopyNumber_[chrCount].addToReadCount(cp); + chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); + normalNumberOfPairs_ += (int)cp; + if (windowSize_ == 0) + windowSize_ = atoi(strs[1].c_str()); + count++; + } + else if (strs.size()==4) { + string chrNumber = strs[0]; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + + if (chrNumber.compare(currentChr)!=0) { + chrCount ++; + currentChr = chrNumber; + chromosomesInd_.insert(pair (currentChr,chrCount)); + chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); + windowSize_ = atoi(strs[2].c_str())-atoi(strs[1].c_str())+1; + } + float cp = (float)strtod(strs[3].c_str(), NULL); + chrCopyNumber_[chrCount].addToReadCount(cp); + chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); + chrCopyNumber_[chrCount].addToEnds(atoi(strs[2].c_str())); + normalNumberOfPairs_ += (int)cp; + if (count>0 && step_==NA) { + // int first = chrCopyNumber_[chrCount].getCoordinateAtBin(0); + // int second = chrCopyNumber_[chrCount].getCoordinateAtBin(1); + step_ = chrCopyNumber_[chrCount].getCoordinateAtBin(1)-chrCopyNumber_[chrCount].getCoordinateAtBin(0); + } - if (windowSize_ == 0) - windowSize_ = atoi(strs[1].c_str()); + if (windowSize_ == 0) + windowSize_ = atoi(strs[1].c_str()); - count++; - } + count++; + } - strs.clear(); - } - file.close(); - cout << "file " << inFile << " read\n"; - if (step_==NA) - step_=windowSize_; - //fill other values - map::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - chrCopyNumber_[(*it).second].setWindowSize(windowSize_); - int length = chrCopyNumber_[(*it).second].getValues().size(); - chrCopyNumber_[(*it).second].setVectorLength(length); - int chromosomeLength=length*step_; - if (chrCopyNumber_[(*it).second].getEndsSize()>0) - chromosomeLength=chrCopyNumber_[(*it).second].getEndAtBin(chrCopyNumber_[(*it).second].getEndsSize()-1); - - chrCopyNumber_[(*it).second].setChrLength(chromosomeLength); - - chrCopyNumber_[(*it).second].setStep(step_); - refGenomeSize_ += chromosomeLength; - //cout <<(*it).first <<"\t" <<(*it).second << "\t" <::iterator it; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + chrCopyNumber_[(*it).second].setWindowSize(windowSize_); + int length = chrCopyNumber_[(*it).second].getValues().size(); + chrCopyNumber_[(*it).second].setVectorLength(length); + int chromosomeLength=length*step_; + if (chrCopyNumber_[(*it).second].getEndsSize()>0) + chromosomeLength=chrCopyNumber_[(*it).second].getEndAtBin(chrCopyNumber_[(*it).second].getEndsSize()-1); + + chrCopyNumber_[(*it).second].setChrLength(chromosomeLength); + + chrCopyNumber_[(*it).second].setStep(step_); + refGenomeSize_ += chromosomeLength; + //cout <<(*it).first <<"\t" <<(*it).second << "\t" < strs = split(line, '\t'); - string chrNumber = strs[0]; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - - if (chrNumber.compare(currentChr)!=0) { - chrCount ++; - currentChr = chrNumber; - chromosomesInd_.insert(pair (currentChr,chrCount)); - chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); - windowSize_ = 0; - } - float cp = (float)strtod(strs[3].c_str(), NULL); - chrCopyNumber_[chrCount].addToReadCount(cp); - chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); - chrCopyNumber_[chrCount].addToEnds(atoi(strs[2].c_str())); - if (strs.size()>=4) + if (WESanalysis == false) {cout << "\t evaluated genome size:\t" << refGenomeSize_ << "\n";} + } else { + totalNumberOfPairs_ = 0; + normalNumberOfPairs_ = 0; + windowSize_ = 0; + ifstream file (inFile.c_str()); + string line; + string currentChr = ""; + int chrCount = -1; + refGenomeSize_ = 0; + string::size_type pos = 0; + int count = 0; + if (file.is_open()) { + while (! file.eof() ) { + getline (file,line); + + if (! line.length()) continue; + + std::vector strs = split(line, '\t'); + string chrNumber = strs[0]; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + + if (chrNumber.compare(currentChr)!=0) { + chrCount ++; + currentChr = chrNumber; + chromosomesInd_.insert(pair (currentChr,chrCount)); + chrCopyNumber_.push_back(ChrCopyNumber(currentChr)); + windowSize_ = 0; + } + float cp = (float)strtod(strs[3].c_str(), NULL); + chrCopyNumber_[chrCount].addToReadCount(cp); + chrCopyNumber_[chrCount].addToCoordinates(atoi(strs[1].c_str())); + chrCopyNumber_[chrCount].addToEnds(atoi(strs[2].c_str())); + if (strs.size()>=4) chrCopyNumber_[chrCount].addToGenes_name(strs[4].c_str()); - normalNumberOfPairs_ += (int)cp; - if (count>0 && step_==NA) { - step_ = 0; - } + normalNumberOfPairs_ += (int)cp; + if (count>0 && step_==NA) { + step_ = 0; + } count++; - strs.clear(); - } - file.close(); - cout << "file " << inFile << " read\n"; - if (step_==NA) - step_=windowSize_; - //fill other values - map::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - chrCopyNumber_[(*it).second].setWindowSize(windowSize_); - int length = chrCopyNumber_[(*it).second].getValues().size(); - chrCopyNumber_[(*it).second].setVectorLength(length); - if (SeekingSubc_ == true) + strs.clear(); + } + file.close(); + cout << "file " << inFile << " read\n"; + if (step_==NA) + step_=windowSize_; + //fill other values + map::iterator it; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + chrCopyNumber_[(*it).second].setWindowSize(windowSize_); + int length = chrCopyNumber_[(*it).second].getValues().size(); + chrCopyNumber_[(*it).second].setVectorLength(length); + if (SeekingSubc_ == true) { - chrCopyNumber_[(*it).second].setCN_subcLength(length+3); - chrCopyNumber_[(*it).second].setpop_subcLength(length+3); + chrCopyNumber_[(*it).second].setCN_subcLength(length+3); + chrCopyNumber_[(*it).second].setpop_subcLength(length+3); } - int chromosomeLength=length*step_; - if (chrCopyNumber_[(*it).second].getEndsSize()>=0) - chromosomeLength=chrCopyNumber_[(*it).second].getEndAtBin(chrCopyNumber_[(*it).second].getEndsSize()-1); + int chromosomeLength=length*step_; + if (chrCopyNumber_[(*it).second].getEndsSize()>=0) + chromosomeLength=chrCopyNumber_[(*it).second].getEndAtBin(chrCopyNumber_[(*it).second].getEndsSize()-1); - chrCopyNumber_[(*it).second].setChrLength(chromosomeLength); + chrCopyNumber_[(*it).second].setChrLength(chromosomeLength); - chrCopyNumber_[(*it).second].setStep(0); - refGenomeSize_ += chrCopyNumber_[(*it).second].getLength(); - //cout <<(*it).first <<"\t" <<(*it).second << "\t" <::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - printCopyNumber((*it).first,file); - } - file.close(); - cout << "printing counts into "<::iterator it; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + printCopyNumber((*it).first,file); + } + file.close(); + cout << "printing counts into "<::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - printCGprofile((*it).first,file); - } - file.close(); - cout << "CG-content printed into "<::iterator it; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + printCGprofile((*it).first,file); + } + file.close(); + cout << "CG-content printed into "<-1) { + std::ofstream file (outFile.c_str()); + for (int i = 0; i < (int)CNVs_.size(); i++) { + if (CNVs_[i].getCopyNumber()>-1) { if (sex_.compare("XY")==0 && (CNVs_[i].getChr().find("X")!=string::npos || CNVs_[i].getChr().find("Y")!=string::npos)) { file << CNVs_[i].printEntryCNV(ploidy_*0.5); - } else { + } else { file << CNVs_[i].printEntryCNV(ploidy_); - } + } file << "\n"; - } - } - file.close(); + } + } + file.close(); } vector GenomeCopyNumber::getCNVs () { @@ -2948,7 +2958,7 @@ void GenomeCopyNumber::calculateSomaticCNVs (std::vector controlCNVs, int overlapPrecision = 3; //+-3 windows => the same CNA - std::cout << "..Calculate somatic CNVs" << std::endl; + std::cout << "..Calculate somatic CNVs" << std::endl; for (int i = 0; i < (int)CNVs_.size(); i++) { string type = "somatic"; vector lefts; @@ -2980,7 +2990,7 @@ void GenomeCopyNumber::calculateSomaticCNVs (std::vector controlCNVs, } else if (type == "somatic") { CNVs_[i].setGermlinePercent(0); } - } + } } void GenomeCopyNumber::printRatioBedGraph(std::string const& chr, std::ofstream & file, std::string const& typeCNA) { @@ -2988,88 +2998,96 @@ void GenomeCopyNumber::printRatioBedGraph(std::string const& chr, std::ofstream float value; int position; string myType; - string chrNumber = chr; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - map::iterator it; - int index = findIndex(chrNumber); - if (index == NA) {return;} - if (!chrCopyNumber_[index].isMedianCalculated()) {cerr << "Error: unable to write a BedGraph with without caclulation of median values..\n"; return;} - int length = chrCopyNumber_[index].getLength(); + string chrNumber = chr; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + map::iterator it; + int index = findIndex(chrNumber); + if (index == NA) {return;} + if (!chrCopyNumber_[index].isMedianCalculated()) {cerr << "Error: unable to write a BedGraph with without caclulation of median values..\n"; return;} + int length = chrCopyNumber_[index].getLength(); if (typeCNA.compare("LOH")==0) { if (!hasBAF_) {cerr << "Error: unable to write LOH in a BedGraph with without caclulation of genotypes..\n"; return;} } for (int i = 0; i< length; i++) { - value=chrCopyNumber_[index].getRatioAtBin(i); - if (isRatioLogged_ && value!=NA) - value=pow(2,value); - position=chrCopyNumber_[index].getCoordinateAtBin(i); - float valueToPrint; - if (chrCopyNumber_[index].isSmoothed()) - valueToPrint = chrCopyNumber_[index].getSmoothedProfileAtI(i)*ploidy_; - else - valueToPrint = round_by_ploidy(chrCopyNumber_[index].getMedianProfileAtI(i),ploidy_)*ploidy_; - - if (valueToPrint<0) - valueToPrint = NA; - if (hasBAF_) { - if (valueToPrint>0 && chrCopyNumber_[index].getBAFsymbolAt(i).compare("-")!=0 &&chrCopyNumber_[index].getBAFsymbolAt(i)!="" && chrCopyNumber_[index].getBAFsymbolAt(i).length()!=valueToPrint ) { //&& (chrCopyNumber_[index].getEstimatedBAFuncertaintyAtI(i)< MAXUncertainty) - valueToPrint=chrCopyNumber_[index].getBAFsymbolAt(i).length(); - } - } - myType="NA"; - if (valueToPrint>ploidy_ && valueToPrint != NA) { - myType = "gain"; - } else if (valueToPrint0 && chrCopyNumber_[index].getBAFsymbolAt(i).compare("-")!=0 &&chrCopyNumber_[index].getBAFsymbolAt(i)!="" && chrCopyNumber_[index].getBAFsymbolAt(i).length()!=valueToPrint ) { //&& (chrCopyNumber_[index].getEstimatedBAFuncertaintyAtI(i)< MAXUncertainty) + valueToPrint=chrCopyNumber_[index].getBAFsymbolAt(i).length(); } - if (myType.compare(typeCNA)==0 && value != NA) - file << "chr" <ploidy_ && valueToPrint != NA) { + myType = "gain"; + } else if (valueToPrint::iterator it; - int index = findIndex(chrNumber); - if (index == NA) {return;} - //cout << "..index found "<::iterator it; + int index = findIndex(chrNumber); + if (index == NA) {return;} + //cout << "..index found "<0 && chrCopyNumber_[index].getBAFsymbolAt(i).compare("-")!=0 &&chrCopyNumber_[index].getBAFsymbolAt(i)!="" && chrCopyNumber_[index].getBAFsymbolAt(i).length()!=valueToPrint ) { //&& (chrCopyNumber_[index].getEstimatedBAFuncertaintyAtI(i)< MAXUncertainty) - //change Level value if there is no incertainty: - valueToPrint=chrCopyNumber_[index].getBAFsymbolAt(i).length(); - } + file << chrNumber <<"\t"<0 && chrCopyNumber_[index].getBAFsymbolAt(i).compare("-")!=0 &&chrCopyNumber_[index].getBAFsymbolAt(i)!="" && chrCopyNumber_[index].getBAFsymbolAt(i).length()!=valueToPrint ) { //&& (chrCopyNumber_[index].getEstimatedBAFuncertaintyAtI(i)< MAXUncertainty) + //change Level value if there is no incertainty: + valueToPrint=chrCopyNumber_[index].getBAFsymbolAt(i).length(); } - file <<"\t"<< valueToPrint; } + file <<"\t"<< valueToPrint; + } + + if (has_smoothed_profile) { + float smoothedRatioToPrint = chrCopyNumber_[index].getSmoothedRatioAtBin(i); + file << "\t" << smoothedRatioToPrint; + float rescaledRatioToPrint = chrCopyNumber_[index].getRescaledRatioAtBin(i); + file << "\t" << rescaledRatioToPrint; + } + if (hasBAF_) { file <<"\t"<< chrCopyNumber_[index].getBAFat(i); file <<"\t"<< (1-chrCopyNumber_[index].getBAFProfileAt(i)); @@ -3081,6 +3099,12 @@ void GenomeCopyNumber::printRatio(std::string const& chr, std::ofstream & file, file <<"\t"<< chrCopyNumber_[index].getEstimatedBAFuncertaintyAtI(i); } + if (has_MAF) { + file <<"\t"<< chrCopyNumber_[index].getSampledBAFat(i); + file <<"\t"<< chrCopyNumber_[index].getSampledMAFat(i); + file << "\t" << chrCopyNumber_[index].getSmoothedMAFat(i); + } + if (WESanalysis == true && chrCopyNumber_[index].getGeneNameAtBin(i)!= "") { file << "\t" << chrCopyNumber_[index].getGeneNameAtBin(i); } @@ -3090,19 +3114,19 @@ void GenomeCopyNumber::printRatio(std::string const& chr, std::ofstream & file, file << "\n"; } - } - cout <<"..writing ratio for " <done!\n"; + } + cout <<"..writing ratio for " <done!\n"; } void GenomeCopyNumber::printBAF(std::string const& chr, std::ofstream & file, SNPatChr& snpAtChrom, std::string myName, std::string const& matefile) { - string::size_type pos = 0; - string chrNumber = chr; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - map::iterator it; - int index = findIndex(chrNumber); - if (index == NA) {return;} - int length = snpAtChrom.getSize(); + string::size_type pos = 0; + string chrNumber = chr; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + map::iterator it; + int index = findIndex(chrNumber); + if (index == NA) {return;} + int length = snpAtChrom.getSize(); for (int i = 0; i< length; i++) { if (snpAtChrom.getStatusAt(i)!=0 && snpAtChrom.getValueAt(i)>=0) { @@ -3114,7 +3138,7 @@ void GenomeCopyNumber::printBAF(std::string const& chr, std::ofstream & file, SN WinNumber = position/step_; } else { WinNumber = snpAtChrom.getBinAt(i); - // findWinNumber(position, myName, matefile); + // findWinNumber(position, myName, matefile); } float Avalue = NA; if (WinNumber!=NA) @@ -3124,7 +3148,7 @@ void GenomeCopyNumber::printBAF(std::string const& chr, std::ofstream & file, SN float Afitted = NA; if (WinNumber!=NA) - Afitted=chrCopyNumber_[index].getFittedBAFProfileAt(WinNumber); + Afitted=chrCopyNumber_[index].getFittedBAFProfileAt(WinNumber); float Bfitted = 1-Afitted; if (Afitted==NA) {Bfitted=NA;} @@ -3132,7 +3156,7 @@ void GenomeCopyNumber::printBAF(std::string const& chr, std::ofstream & file, SN } } - cout <<"..writing BAF profiles for " <done!\n"; + cout <<"..writing BAF profiles for " <done!\n"; } /* int GenomeCopyNumber::findWinNumber(int position, std::string myName, std::string const& matefile) @@ -3168,15 +3192,15 @@ int GenomeCopyNumber::findWinNumber(int position, std::string myName, std::strin } */ void GenomeCopyNumber::printCGprofile(std::string const& chr, std::ofstream & file) { - string::size_type pos = 0; - string chrNumber = chr; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - map::iterator it; - int index = findIndex(chrNumber); - if (index == NA) {return;} - int length = chrCopyNumber_[index].getLength(); - if (chrCopyNumber_[index].getMappabilityLength()>0) + string::size_type pos = 0; + string chrNumber = chr; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + map::iterator it; + int index = findIndex(chrNumber); + if (index == NA) {return;} + int length = chrCopyNumber_[index].getLength(); + if (chrCopyNumber_[index].getMappabilityLength()>0) for (int i = 0; i< length; i++) file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getCGprofileAt(i) <<"\t"<::iterator it; - int index = findIndex(chrNumber); - if (index == NA) {return;} - int length = chrCopyNumber_[index].getLength(); - if (WESanalysis != false) - { + string::size_type pos = 0; + string chrNumber = chr; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + map::iterator it; + int index = findIndex(chrNumber); + if (index == NA) {return;} + int length = chrCopyNumber_[index].getLength(); + if (WESanalysis != false) + { for (int i = 0; i< length; i++) file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getEndAtBin(i) <<"\t"<< chrCopyNumber_[index].getValueAt(i) << "\t" << chrCopyNumber_[index].getGeneNameAtBin(i) << "\n"; - } + } else { - if (windowSize_ == step_) { - for (int i = 0; i< length; i++) - file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getValueAt(i) << "\n"; - } else { - for (int i = 0; i< length; i++) - file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getEndAtBin(i) <<"\t"<< chrCopyNumber_[index].getValueAt(i) << "\n"; - } - } + if (windowSize_ == step_) { + for (int i = 0; i< length; i++) + file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getValueAt(i) << "\n"; + } else { + for (int i = 0; i< length; i++) + file << chrNumber <<"\t"<< chrCopyNumber_[index].getCoordinateAtBin(i) <<"\t"<< chrCopyNumber_[index].getEndAtBin(i) <<"\t"<< chrCopyNumber_[index].getValueAt(i) << "\n"; + } + } } void GenomeCopyNumber::calculateCopyNumberMedians (int minCNAlength, bool noisyData, bool CompleteGenomicsData) { - cout << "..calculating medians for copy numbers\n"; - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + cout << "..calculating medians for copy numbers\n"; + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { cout << "..calculating medians for " << it->getChromosome()<< "\n"; - it->calculateCopyNumberMedian(ploidy_, minCNAlength, noisyData, CompleteGenomicsData, isRatioLogged_); - } + it->calculateCopyNumberMedian(ploidy_, minCNAlength, noisyData, CompleteGenomicsData, isRatioLogged_); + } } void GenomeCopyNumber::shiftNeutalRatioTo1() { @@ -3225,196 +3249,196 @@ void GenomeCopyNumber::shiftNeutalRatioTo1() { } void GenomeCopyNumber::calculatePloidy(int minCNAlength) { - //check if median for copy numbers is calculated - if (chrCopyNumber_[0].getMedianValues().size()==0) - calculateCopyNumberMedians(minCNAlength,0,0); - cout << "..Getting ploidy information\n"; - int ploidy[] = {1,2,3,4,5,6,7,8,9,10}; - vector scores; - for (int i = 0; i < 6 ; i++) { - scores.push_back(calculateXiSum(ploidy[i])); - } - int i = argmin(scores); - ploidy_ = ploidy[i]; - cout << "..selected ploidy: " < scores; + for (int i = 0; i < 6 ; i++) { + scores.push_back(calculateXiSum(ploidy[i])); + } + int i = argmin(scores); + ploidy_ = ploidy[i]; + cout << "..selected ploidy: " < sds; - //map meds; - //float varZero = calculateVarianceForNormalCopy(ploidy); - //calculateSDAndMed(ploidy,sds,meds); - calculateSDs(ploidy,sds); - vector::iterator it; - cout << "..Calculating sum of squares for ploidy = "<getChromosome()<<"\n"; - totalNumberOfBP += it->getNumberOfGoodFragments(); - //totalSum += it->getXiSum(ploidy,sqrt(varZero)); - //totalSum += it->calculateXiSum(ploidy,sds,meds); - totalSum += it->calculateXiSum(ploidy,sds); - } - sds.clear(); - //meds.clear(); - cout << "ploidy\t" << ploidy << "\ttest-value\t"< sds; + //map meds; + //float varZero = calculateVarianceForNormalCopy(ploidy); + //calculateSDAndMed(ploidy,sds,meds); + calculateSDs(ploidy,sds); + vector::iterator it; + cout << "..Calculating sum of squares for ploidy = "<getChromosome()<<"\n"; + totalNumberOfBP += it->getNumberOfGoodFragments(); + //totalSum += it->getXiSum(ploidy,sqrt(varZero)); + //totalSum += it->calculateXiSum(ploidy,sds,meds); + totalSum += it->calculateXiSum(ploidy,sds); + } + sds.clear(); + //meds.clear(); + cout << "ploidy\t" << ploidy << "\ttest-value\t"< &sds,map &meds) { - float value,med; - vector::iterator it; - - //fill the map - map > mymap; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - for (int i = 0; igetLength(); i++) { - med = it->getMedianProfileAtI(i); - float level = round_by_ploidy(med, ploidy); - value = it->getRatioAtBin(i); - if (isRatioLogged_&& value!=NA) + float value,med; + vector::iterator it; + + //fill the map + map > mymap; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + for (int i = 0; igetLength(); i++) { + med = it->getMedianProfileAtI(i); + float level = round_by_ploidy(med, ploidy); + value = it->getRatioAtBin(i); + if (isRatioLogged_&& value!=NA) value=pow(2,value); - if (value != NA) { - if (mymap.count(level) == 0) { - vector a; - mymap.insert ( pair >(level,a) ); - } - mymap.find(level)->second.push_back(value); - } - } - } + if (value != NA) { + if (mymap.count(level) == 0) { + vector a; + mymap.insert ( pair >(level,a) ); + } + mymap.find(level)->second.push_back(value); + } + } + } - //get median and variance for each level - map >::iterator it2; - for ( it2=mymap.begin() ; it2 != mymap.end(); it2++ ) { - float level = (*it2).first; - float median = get_median((*it2).second); - // float mean = get_mean((*it2).second); - float sdev = sd((*it2).second,median); - meds.insert(pair(level,median)); - sds.insert(pair(level,sdev)); - (*it2).second.clear(); - } - mymap.clear(); + //get median and variance for each level + map >::iterator it2; + for ( it2=mymap.begin() ; it2 != mymap.end(); it2++ ) { + float level = (*it2).first; + float median = get_median((*it2).second); + // float mean = get_mean((*it2).second); + float sdev = sd((*it2).second,median); + meds.insert(pair(level,median)); + sds.insert(pair(level,sdev)); + (*it2).second.clear(); + } + mymap.clear(); } void GenomeCopyNumber::calculateSDs(int ploidy, map &sds) { - float value,med; - vector::iterator it; - - //fill the map - map > mymap; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - for (int i = 0; igetLength(); i++) { - med = it->getMedianProfileAtI(i); - float level = round_by_ploidy(med, ploidy); - value = it->getRatioAtBin(i); - if (isRatioLogged_&& value!=NA) + float value,med; + vector::iterator it; + + //fill the map + map > mymap; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + for (int i = 0; igetLength(); i++) { + med = it->getMedianProfileAtI(i); + float level = round_by_ploidy(med, ploidy); + value = it->getRatioAtBin(i); + if (isRatioLogged_&& value!=NA) value=pow(2,value); - if (value != NA) { - if (mymap.count(level) == 0) { - vector a; - mymap.insert ( pair >(level,a) ); - } - mymap.find(level)->second.push_back(value); - } - } - } + if (value != NA) { + if (mymap.count(level) == 0) { + vector a; + mymap.insert ( pair >(level,a) ); + } + mymap.find(level)->second.push_back(value); + } + } + } - //get median and variance for each level - map >::iterator it2; - for ( it2=mymap.begin() ; it2 != mymap.end(); it2++ ) { - float level = (*it2).first; - // float mean = get_mean((*it2).second); - float sdev = sd((*it2).second,level); - sds.insert(pair(level,sdev)); - (*it2).second.clear(); - } - mymap.clear(); + //get median and variance for each level + map >::iterator it2; + for ( it2=mymap.begin() ; it2 != mymap.end(); it2++ ) { + float level = (*it2).first; + // float mean = get_mean((*it2).second); + float sdev = sd((*it2).second,level); + sds.insert(pair(level,sdev)); + (*it2).second.clear(); + } + mymap.clear(); } float GenomeCopyNumber::calculateVarianceForNormalCopy(int ploidy) { //geting the total variance for points with median around 1 (+-0.5/ploidy) --- OLD - float variance = 0; - int count = 0; - double lowBoundary = 1-0.5/ploidy; - double highBoundary = 1+0.5/ploidy; - float value,med; - vector::iterator it; - - ofstream myfile; - - myfile.open ("example.txt"); - - - cout << "..Calculating variance for neutral copies\n"; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - //cout << "..processing chromosome " <getChromosome()<<"\n"; - for (int i = 0; igetLength(); i++) { - med = it->getMedianProfileAtI(i); - if ((med>lowBoundary)&&(med < highBoundary)) { - value = it->getRatioAtBin(i); - if (isRatioLogged_&& value!=NA) + float variance = 0; + int count = 0; + double lowBoundary = 1-0.5/ploidy; + double highBoundary = 1+0.5/ploidy; + float value,med; + vector::iterator it; + + ofstream myfile; + + myfile.open ("example.txt"); + + + cout << "..Calculating variance for neutral copies\n"; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + //cout << "..processing chromosome " <getChromosome()<<"\n"; + for (int i = 0; igetLength(); i++) { + med = it->getMedianProfileAtI(i); + if ((med>lowBoundary)&&(med < highBoundary)) { + value = it->getRatioAtBin(i); + if (isRatioLogged_&& value!=NA) value=pow(2,value); - if (value != NA) { - myfile << value-1 << "\n"; - variance += (value-1)*(value-1); - count++; - } - } - } - } - myfile.close(); - return float(variance/(count-1)); + if (value != NA) { + myfile << value-1 << "\n"; + variance += (value-1)*(value-1); + count++; + } + } + } + } + myfile.close(); + return float(variance/(count-1)); } void GenomeCopyNumber::printPloidy(std::string const& outFile) { - std::ofstream file (outFile.c_str()); - printPloidy(file); - file.close(); + std::ofstream file (outFile.c_str()); + printPloidy(file); + file.close(); } void GenomeCopyNumber::printPloidy(std::ofstream & file) { - file << "Sample ploidy is " << ploidy_ << " with p-value " << ploidy_pvalue_ << std::endl; + file << "Sample ploidy is " << ploidy_ << " with p-value " << ploidy_pvalue_ << std::endl; } void GenomeCopyNumber::fillCGprofile(std::string const& chrFolder) { - //reading the file with genome information - vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - it->fillCGprofile(chrFolder); - } + //reading the file with genome information + vector::iterator it; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + it->fillCGprofile(chrFolder); + } } float GenomeCopyNumber::evaluateContamination () { - float contam = 0; - string::size_type pos = 0; - vector values; + float contam = 0; + string::size_type pos = 0; + vector values; vector weights; - map::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - string chrNumber = (*it).first; - if ( ( pos = chrNumber.find("chr")) != string::npos ) - chrNumber.replace( pos, 3, "" ); + map::iterator it; + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + string chrNumber = (*it).first; + if ( ( pos = chrNumber.find("chr")) != string::npos ) + chrNumber.replace( pos, 3, "" ); if ( ( pos = chrNumber.find("X")) != string::npos ) //exclude X and Y from the analysis continue; if ( ( pos = chrNumber.find("Y")) != string::npos ) continue; - int index = findIndex(chrNumber); - if (index == NA) { - cerr << "An error occurred in GenomeCopyNumber::evaluateContamination: could not find an index for "< observed_values; + string::size_type pos = 0; + vector observed_values; vector expected_values; - map::iterator it; + map::iterator it; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - string chrNumber = (*it).first; - if ( ( pos = chrNumber.find("chr")) != string::npos ) - chrNumber.replace( pos, 3, "" ); + for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + string chrNumber = (*it).first; + if ( ( pos = chrNumber.find("chr")) != string::npos ) + chrNumber.replace( pos, 3, "" ); if ( ( pos = chrNumber.find("X")) != string::npos ) //exclude X and Y from the analysis continue; if ( ( pos = chrNumber.find("Y")) != string::npos ) continue; - int index = findIndex(chrNumber); - if (index == NA) { - cerr << "An error occurred in GenomeCopyNumber::evaluateContamination: could not find an index for "< x = expected_values; vector y = observed_values; @@ -3505,12 +3529,12 @@ float GenomeCopyNumber::evaluateContaminationwithLR () { float a = (n * sum_xy - sum_x * sum_y) / (n * sum_x2 - sum_x * sum_x); //CARINO a =sum_xy/sum_x2; //VALENTINA - // float b = (sum_x2 * sum_y - sum_x * sum_xy) / (n * sum_x2 - sum_x * sum_x); + // float b = (sum_x2 * sum_y - sum_x * sum_xy) / (n * sum_x2 - sum_x * sum_x); float contam_a = (1-a)/(1-a+2*a/(float)ploidy_); - // float contam_b = -b/(-b+(2*b/ploidy_)-(2/ploidy_)); - /*cerr << a << "\t" << b << "\n"; - cerr << contam_a << "\t" << contam_b;*/ - // contam = 2*(1 - a); //contam_a/2 + contam_b/2; CARINO + // float contam_b = -b/(-b+(2*b/ploidy_)-(2/ploidy_)); + /*cerr << a << "\t" << b << "\n"; + cerr << contam_a << "\t" << contam_b;*/ + // contam = 2*(1 - a); //contam_a/2 + contam_b/2; CARINO if (contam_a<0) { cout << "\t..Evaluation of contamination produced a negative value: "<::iterator it; + string::size_type pos = 0; + map::iterator it; hasBAF_=true; - for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { - string chrNumber = (*it).first; - if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) - chrNumber.replace( pos, 3, "" ); - int index = findIndex(chrNumber); - if (index == NA) { - cerr << "An error occurred in GenomeCopyNumber::addBAFinfo: could not find an index for "< (chrCopyNumber_[index].getCoordinateAtBin(l) - insert_size)))) { leftIsInTheWindow = true; @@ -3830,7 +3854,7 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates } } if (!leftIsInTheWindow) { - //start from the beginning of the chromosome + //start from the beginning of the chromosome for (l=0; left>=chrCopyNumber_[index].getCoordinateAtBin(l)- 30*insert_size && l (chrCopyNumber_[index].getCoordinateAtBin(l) - insert_size)))) { leftIsInTheWindow = true; @@ -3986,8 +4010,8 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates leftIsInTheWindow = true; } else { while ((!((left - 1 < chrCopyNumber_[index].getEndAtBin(l)) && - (left > (chrCopyNumber_[index].getCoordinateAtBin(l) - read_Size)))) && - (l < chrCopyNumber_[index].getExons_Countchr())) { + (left > (chrCopyNumber_[index].getCoordinateAtBin(l) - read_Size)))) && + (l < chrCopyNumber_[index].getExons_Countchr())) { leftIsInTheWindow = false; l++; } if (l < chrCopyNumber_[index].getExons_Countchr() -1 ) { @@ -4016,16 +4040,16 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates int left, right,insertSize; if (getELANDinfo(line_buffer,chr1,chr2,orient1,orient2,left,right,insertSize)) { - MateOrientation orient1_2 = getMateOrientation(orient1+orient2); - MateOrientation orient2_1 = getMateOrientation(orient2+orient1); - if ((matesOrientation == orient1_2 && insertSize>0) || (matesOrientation == orient2_1 && insertSize<0)) { - // EV: warning orient2_1 not used: port "as is" from 5.9 version, bug ? - it was a bug! Valentina - int ind = findIndex(chr1); - if (ind!=NA) { - chrCopyNumber_[ind].mappedPlusOneAtI(min(left,right), step_); - valueToReturn= 1; + MateOrientation orient1_2 = getMateOrientation(orient1+orient2); + MateOrientation orient2_1 = getMateOrientation(orient2+orient1); + if ((matesOrientation == orient1_2 && insertSize>0) || (matesOrientation == orient2_1 && insertSize<0)) { + // EV: warning orient2_1 not used: port "as is" from 5.9 version, bug ? - it was a bug! Valentina + int ind = findIndex(chr1); + if (ind!=NA) { + chrCopyNumber_[ind].mappedPlusOneAtI(min(left,right), step_); + valueToReturn= 1; + } } - } } return valueToReturn; } @@ -4033,14 +4057,14 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates if (inputFormat == BOWTIE_INPUT_FORMAT && matesOrientation == SINGLE_END_SORTED_SAM) { std::vector strs = split(line_buffer, '\t'); if (strs.size() > 4) { - string chr = strs[2]; - processChrName(chr); - int index = findIndex(chr); - if (index!=NA) { - int left = atoi(strs[3].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left, step_); - valueToReturn= 1; - } + string chr = strs[2]; + processChrName(chr); + int index = findIndex(chr); + if (index!=NA) { + int left = atoi(strs[3].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left, step_); + valueToReturn= 1; + } } strs.clear(); return valueToReturn; @@ -4049,14 +4073,14 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates if (inputFormat == PSL_INPUT_FORMAT && matesOrientation == SINGLE_END_SORTED_SAM) { std::vector strs = split(line_buffer, '\t'); if (strs.size() > 17) { - string chr = strs[13]; - processChrName(chr); - int index = findIndex(chr); - if (index!=NA) { - int left = atoi(strs[15].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left,step_); - valueToReturn= 1; - } + string chr = strs[13]; + processChrName(chr); + int index = findIndex(chr); + if (index!=NA) { + int left = atoi(strs[15].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left,step_); + valueToReturn= 1; + } } strs.clear(); return valueToReturn; @@ -4065,27 +4089,27 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates if (inputFormat == ARACHNE_BED_INPUT_FORMAT && matesOrientation == SINGLE_END_SORTED_SAM) { std::vector strs = split(line_buffer, '\t'); if (strs.size() > 1) { - string chr = strs[0]; - processChrName(chr); - int index = findIndex(chr); - if (index!=NA){ - int left = atoi(strs[1].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left,step_); - valueToReturn= 1; - } - } else { - strs.clear(); - strs = split(line_buffer, ' '); - if (strs.size() > 1) { string chr = strs[0]; processChrName(chr); int index = findIndex(chr); - if (index!=NA) { - int left = atoi(strs[1].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left,step_); - valueToReturn= 1; + if (index!=NA){ + int left = atoi(strs[1].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left,step_); + valueToReturn= 1; + } + } else { + strs.clear(); + strs = split(line_buffer, ' '); + if (strs.size() > 1) { + string chr = strs[0]; + processChrName(chr); + int index = findIndex(chr); + if (index!=NA) { + int left = atoi(strs[1].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left,step_); + valueToReturn= 1; + } } - } } strs.clear(); return valueToReturn; @@ -4094,14 +4118,14 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates if (inputFormat == SOAP_INPUT_FORMAT && matesOrientation == SINGLE_END_SORTED_SAM) { std::vector strs = split(line_buffer, '\t'); if (strs.size() > 8) { - string chr = strs[7]; - processChrName(chr); - int index = findIndex(chr); - if (index!=NA) { - int left = atoi(strs[8].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left,step_); - valueToReturn= 1; - } + string chr = strs[7]; + processChrName(chr); + int index = findIndex(chr); + if (index!=NA) { + int left = atoi(strs[8].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left,step_); + valueToReturn= 1; + } } strs.clear(); return valueToReturn; @@ -4110,14 +4134,14 @@ int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation mates if (inputFormat == SOAP_INPUT_FORMAT && matesOrientation != SINGLE_END_SORTED_SAM) { std::vector strs = split(line_buffer, '\t'); if (strs.size() > 8) { - string chr = strs[7]; - processChrName(chr); - int index = findIndex(chr); - if (index!=NA) { - int left = atoi(strs[8].c_str()); - chrCopyNumber_[index].mappedPlusOneAtI(left,step_); - valueToReturn= 1; - } + string chr = strs[7]; + processChrName(chr); + int index = findIndex(chr); + if (index!=NA) { + int left = atoi(strs[8].c_str()); + chrCopyNumber_[index].mappedPlusOneAtI(left,step_); + valueToReturn= 1; + } } strs.clear(); return valueToReturn; @@ -4134,71 +4158,71 @@ int GenomeCopyNumber::processReadWithBowtie(std::string const& inputFormat, std: string chr1, chr2, orient1, orient2; - if ((inputFormat.compare("bowtie")==0 || inputFormat.compare("Bowtie")==0)&&(matesOrientation.compare("0")!=0)){ + if ((inputFormat.compare("bowtie")==0 || inputFormat.compare("Bowtie")==0)&&(matesOrientation.compare("0")!=0)){ - if (! line2.length()) return 0; - std::vector strs = split(line, '\t'); - std::vector strs2 = split(line2, '\t'); - if ((strs.size() > 4)&&(strs2.size() > 4)) { - string chr1 = strs[2]; - string chr2 = strs2[2]; - - processChrName(chr1); - processChrName(chr2); - if (chr1.compare(chr2)==0) { - - string orient1 = strs[1]; - string orient2 = strs2[1]; - if (orient1.compare("+")==0) - orient1 = "F"; - else - orient1 = "R"; + if (! line2.length()) return 0; + std::vector strs = split(line, '\t'); + std::vector strs2 = split(line2, '\t'); + if ((strs.size() > 4)&&(strs2.size() > 4)) { + string chr1 = strs[2]; + string chr2 = strs2[2]; + + processChrName(chr1); + processChrName(chr2); + if (chr1.compare(chr2)==0) { + + string orient1 = strs[1]; + string orient2 = strs2[1]; + if (orient1.compare("+")==0) + orient1 = "F"; + else + orient1 = "R"; - if (orient2.compare("+")==0) - orient2 = "F"; - else - orient2 = "R"; - int left = atoi(strs[3].c_str()); - int right = atoi(strs2[3].c_str()); + if (orient2.compare("+")==0) + orient2 = "F"; + else + orient2 = "R"; + int left = atoi(strs[3].c_str()); + int right = atoi(strs2[3].c_str()); - if ((matesOrientation.compare(orient1+orient2)==0 && (right-left>0)) || (matesOrientation.compare(orient2+orient1)==0 && (right-left<0))) { - int index = findIndex(chr1); - if (index!=NA) { - chrCopyNumber_[index].mappedPlusOneAtI(min(left,right),step_); - valueToReturn=1; - } + if ((matesOrientation.compare(orient1+orient2)==0 && (right-left>0)) || (matesOrientation.compare(orient2+orient1)==0 && (right-left<0))) { + int index = findIndex(chr1); + if (index!=NA) { + chrCopyNumber_[index].mappedPlusOneAtI(min(left,right),step_); + valueToReturn=1; } } - } - strs.clear(); - strs2.clear(); - return valueToReturn; - } - return 0; + } + } + strs.clear(); + strs2.clear(); + return valueToReturn; + } + return 0; } float GenomeCopyNumber::removeLargeExons(float iqrToKeep) { float maxLength = 0; - vector::iterator it; - int totalNumberExons=0; - float numberOfRemovedExons = 0; - vector exonLengths; + vector::iterator it; + int totalNumberExons=0; + float numberOfRemovedExons = 0; + vector exonLengths; for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { for (int i=0; i < it->getLength(); i++) { exonLengths.push_back(it->getEndAtBin(i)-it->getCoordinateAtBin(i)); totalNumberExons++; } - } + } maxLength=get_iqr(exonLengths)/2*iqrToKeep+get_median(exonLengths); for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { numberOfRemovedExons+=it->removeLargeExons(maxLength); - } - return numberOfRemovedExons/totalNumberExons; + } + return numberOfRemovedExons/totalNumberExons; } int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) { - ifstream file (captureFile.c_str()); - string line; + ifstream file (captureFile.c_str()); + string line; //string::size_type pos = 0; string currentChr = ""; int index = NA; @@ -4214,29 +4238,29 @@ int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) { int averageReadLength=400; averageReadLength=150;//from version 6.6 - if (file.is_open()) { - cout << "..Reading "<< captureFile << "\n"; + if (file.is_open()) { + cout << "..Reading "<< captureFile << "\n"; cout << "..Your file must be in .BED format, and it must be sorted\n"; - while (! file.eof() ) { - getline (file,line); - if (! line.length()) continue; + while (! file.eof() ) { + getline (file,line); + if (! line.length()) continue; std::vector strs = split(line, '\t'); if (strs.size()<3) continue; - string chr = strs[0]; + string chr = strs[0]; processChrName(chr); int positionS = atoi(strs[1].c_str())-averageReadLength; if (positionS<=0) positionS=1; int positionE = atoi(strs[2].c_str())-1; //because it is 1-based if (positionS >= positionE || positionS<0) continue; - if ( currentChr.compare(chr)!=0 ){ //start reading a new chromosome + if ( currentChr.compare(chr)!=0 ){ //start reading a new chromosome cout << "..Reading capture for chromosome " << chr << "\n"; index = findIndex(chr); if (index == NA) { - cout << "skipping chromosome " << chr << "\n"; - continue; + cout << "skipping chromosome " << chr << "\n"; + continue; } //restore all variables for a new chromosome currentChr = chr; @@ -4251,7 +4275,7 @@ int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) { //check is notNprofile_ exists, and create it if it does not exists: chrCopyNumber_[index].checkOrCreateNotNprofileWithZeros(); //cout << "..Index for chromosome " << currentChr << ": "<< index << "\n"; - } + } count ++; int leftWindow = positionS/step_; @@ -4272,29 +4296,29 @@ int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) { ratio = float(mapCount)/windowSize_; chrCopyNumber_[index].setNotNprofileAt(i, ratio); } - } - file.close(); - cout << "file " << captureFile << " is read\n"; - } else{ + } + file.close(); + cout << "file " << captureFile << " is read\n"; + } else{ cerr << "Error: Unable to open file "+captureFile+"\n"; exit(-1); - } + } //EXCLUDE all windows that are not in capture cout << "..Setting read counts to Zero for all windows outside of capture\n"; vector::iterator it=chrCopyNumber_.begin(); cout << "..Total size of captured regions "<< refGenomeSize_<<"bp\n"; - for ( ; it != chrCopyNumber_.end(); it++ ) { - cout << "..processing chromosome " <getChromosome()<<"\n"; - it->setRCountToZeroForNNNN(); - } + for ( ; it != chrCopyNumber_.end(); it++ ) { + cout << "..processing chromosome " <getChromosome()<<"\n"; + it->setRCountToZeroForNNNN(); + } return int(minRegion); } void GenomeCopyNumber::setSamtools(std::string const& pathToSamtools, std::string const& SambambaThreads) { pathToSamtools_=pathToSamtools; - SambambaThreads_ = SambambaThreads; + SambambaThreads_ = SambambaThreads; } void GenomeCopyNumber::setReference(std::string const& pathToReference) { @@ -4313,7 +4337,7 @@ bool GenomeCopyNumber::getWESanalysis() void GenomeCopyNumber::setWESanalysis(bool WESgiven) { -WESanalysis = WESgiven; + WESanalysis = WESgiven; } void GenomeCopyNumber::setIfLogged(bool isRatioLogged) { @@ -4322,7 +4346,7 @@ void GenomeCopyNumber::setIfLogged(bool isRatioLogged) { void GenomeCopyNumber::setmakingPileup(bool makingPileup_given) { -makingPileup = makingPileup_given; + makingPileup = makingPileup_given; } @@ -4330,42 +4354,67 @@ void GenomeCopyNumber::setSeekSubclones(bool seekSubclones) { SeekingSubc_ = seekSubclones; vector::iterator it; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) - it->setLookingForSubclones(seekSubclones); + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) + it->setLookingForSubclones(seekSubclones); +} + +void GenomeCopyNumber::setDataSubsamplingRateInPuritySearch(int _dataSubsamplingRateInPuritySearch) +{ + dataSubsamplingRateInPuritySearch = _dataSubsamplingRateInPuritySearch; +} + +void GenomeCopyNumber::setDataSubsamplingRateInPloidyEvaluation(int _dataSubsamplingRateInPloidyEvaluation) +{ + dataSubsamplingRateInPloidyEvaluation = _dataSubsamplingRateInPloidyEvaluation; +} + +int GenomeCopyNumber::getDataSubsamplingRateInPuritySearch() +{ + return dataSubsamplingRateInPuritySearch; +} + +int GenomeCopyNumber::getDataSubsamplingRateInPloidyEvaluation() +{ + return dataSubsamplingRateInPloidyEvaluation; +} + +void GenomeCopyNumber::setDoRescaleRatio(bool _doRescaleRatio) +{ + doRescaleRatio = _doRescaleRatio; } void* GenomeCopyNumber_readMateFile_wrapper(void *arg) { - GenomeCopyNumberReadMateFileArgWrapper* warg = (GenomeCopyNumberReadMateFileArgWrapper*)arg; - if (warg->p_genomeCopyNumber) { - warg->snpInGenome.readMateFile(warg->mateFile, warg->inputFormat, warg->minimalTotalLetterCountPerPosition, warg->minimalQualityPerPosition, *warg->p_genomeCopyNumber, warg->chrLenFileName, warg->windowSize, warg->step, warg->targetBed); - } else { - warg->snpInGenome.readMateFile(warg->mateFile, warg->inputFormat, warg->minimalTotalLetterCountPerPosition, warg->minimalQualityPerPosition); - } - return NULL; + GenomeCopyNumberReadMateFileArgWrapper* warg = (GenomeCopyNumberReadMateFileArgWrapper*)arg; + if (warg->p_genomeCopyNumber) { + warg->snpInGenome.readMateFile(warg->mateFile, warg->inputFormat, warg->minimalTotalLetterCountPerPosition, warg->minimalQualityPerPosition, *warg->p_genomeCopyNumber, warg->chrLenFileName, warg->windowSize, warg->step, warg->targetBed); + } else { + warg->snpInGenome.readMateFile(warg->mateFile, warg->inputFormat, warg->minimalTotalLetterCountPerPosition, warg->minimalQualityPerPosition); + } + return NULL; } void* GenomeCopyNumber_calculateBreakpoint_wrapper(void *arg) { - GenomeCopyNumberCalculateBreakpointArgWrapper* warg = (GenomeCopyNumberCalculateBreakpointArgWrapper*)arg; - warg->genomeCopyNumber.calculateBreakpoints(warg->breakPointThreshold, warg->breakPointType); - return NULL; + GenomeCopyNumberCalculateBreakpointArgWrapper* warg = (GenomeCopyNumberCalculateBreakpointArgWrapper*)arg; + warg->genomeCopyNumber.calculateBreakpoints(warg->breakPointThreshold, warg->breakPointType); + return NULL; } double GenomeCopyNumber::Percentage_GenomeExplained(int & unexplainedChromosomes) { - vector::iterator it; - long double fragment_median2 ; - long double numberOfPoints=0; - double sum_frags = 0; - unexplainedChromosomes=0; + vector::iterator it; + long double fragment_median2 ; + long double numberOfPoints=0; + double sum_frags = 0; + unexplainedChromosomes=0; bool unexplained=0; int threshold = 10; - for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { - if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { - int fragmentLength=0; - if (unexplained)unexplainedChromosomes++; + for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { + if (! (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) { + int fragmentLength=0; + if (unexplained)unexplainedChromosomes++; unexplained=0; for (int i = 0; i< it->getNumberOfFragments(); i++) { // for each fragment: fragment_median2 = it->getMedianValuesAt(i); @@ -4374,13 +4423,331 @@ double GenomeCopyNumber::Percentage_GenomeExplained(int & unexplainedChromosomes numberOfPoints+=fragmentLength; if (fragment_median2!=NA && abs(fragment_median2-round_by_ploidy(fragment_median2,ploidy_)) >= 1.0/3/ploidy_) { //cout << "Unexplained segment: "< bins(ceil((max_el+0.01)/0.01)); + float x = 0; + std::generate(bins.begin(), bins.end(), [&]{return x+=0.01;}); + std::cout << "/* for(auto x : bins) */" << std::endl; + for(auto x : bins) + { + std::cout << x << std::endl; + } + std::vector counts = makeHistogramOfCounts(total_ratio, bins); + std::cout << "Counts: "; + for (float c : counts) { + std::cout << c << " "; + } + std::cout << std::endl; + std::map peaks = findPeaks(counts, 2, 50, 20); + int peak_pos = 0; + float peak_value = 0; + for (std::map::iterator it = peaks.begin(); it != peaks.end(); ++it) { + if (it->second > peak_value) { + peak_value = it->second; + peak_pos = it->first; + } + } + float peak = bins[peak_pos]; + return peak; +} + +void GenomeCopyNumber::rescaleRatio() +{ + std::vector total_ratio; + int count_ratios=0; + for (unsigned int i = 0; i < chrCopyNumber_.size(); i++) { + for (unsigned int j = 0; j < chrCopyNumber_[i].getSmoothedRatioSize(); j++) { + count_ratios++; + if (i>=chrCopyNumber_[i].getSmoothedRatioSize()) continue; + float r = chrCopyNumber_[i].getSmoothedRatioAtBin(j); + if ((r != -1) & (r < 3)) { + total_ratio.push_back(r); + } + } + } + std::cout << "rescaleRatio: total_ratio size: " << total_ratio.size() << std::endl; + std::cout << "rescaleRatio: total_ratio size / all ratios: " << (float)total_ratio.size() / count_ratios << std::endl; + float peak; + if (doRescaleRatio){ + peak = findMaximumPeak(total_ratio); + } else { + peak = 1; + } + std::cout << "Peak: " << peak << std::endl; + for (unsigned int i = 0; i < chrCopyNumber_.size(); i++) { + chrCopyNumber_[i].rescaleRatio(peak); + } +} + +void GenomeCopyNumber::preprocessing(SNPinGenome& snpingenome) +{ + for (unsigned int i = 0; i < chrCopyNumber_.size(); i++) { + chrCopyNumber_[i].createRatioAndBAFFromSNPs(snpingenome); + chrCopyNumber_[i].transformBAFtoMAF(); + chrCopyNumber_[i].smoothRatioBySegments(); + } + rescaleRatio(); + for (unsigned int i = 0; i < chrCopyNumber_.size(); i++) { + chrCopyNumber_[i].simpleExponentialSmoothingMAF(); + chrCopyNumber_[i].filterRatioAndMAF(); + } +} + +void GenomeCopyNumber::printRatioAfterPreprocessing(std::string const& outFile) +{ + std::ofstream file (outFile.c_str()); + map::iterator it; + + file << "Chromosome\tRatio\tSmoothedRatio\tRescaledRatio\tMedianRatio\tBAF\tMAF\tSmoothedMAF"; + file << "\n"; + for (it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + string::size_type pos = 0; + string chr = (*it).first; + string chrNumber = chr; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) + chrNumber.replace( pos, 3, "" ); + int index = findIndex(chrNumber); + if (index == NA) {return;} + int length = chrCopyNumber_[index].getSNPLength(); + for (int i = 0; i < length; i++) { + float ratioToPrint = chrCopyNumber_[index].getRatioPerSNPat(i); + /*if (isRatioLogged_ && ratioToPrint!= NA) { + ratioToPrint=pow(2,ratioToPrint); + }*/ + if (ratioToPrint!=NA) { + file << chrNumber << "\t" << ratioToPrint; + float smoothedRatioToPrint = chrCopyNumber_[index].getSmoothedRatioAtBin(i); + float rescaledRatioToPrint = chrCopyNumber_[index].getRescaledRatioAtBin(i); + float medianRatioToPrint = chrCopyNumber_[index].getMedianRatioPerSNPat(i); + file << "\t" << smoothedRatioToPrint << "\t" << rescaledRatioToPrint << "\t" << medianRatioToPrint; + //int positionToPrint = chrCopyNumber_[index].getSNPPositionAt(i); + float BAFtoPrint = chrCopyNumber_[index].getBAFPerSNPat(i); + float MAFtoPrint = chrCopyNumber_[index].getMAFPerSNPat(i); + float smoothedMAFtoPrint = chrCopyNumber_[index].getSmoothedMAFat(i); + file << "\t" << BAFtoPrint << "\t" << MAFtoPrint << "\t" << smoothedMAFtoPrint; + file << "\n"; + } + } + cout <<"..writing ratio for " << chr <<"->done!\n"; + } + file.close(); +} + +float GenomeCopyNumber::getFilteredRatio(int index, int i) +{ + return chrCopyNumber_[index].getFilteredRatioAt(i); +} + +float GenomeCopyNumber::getFilteredMAF(int index, int i) +{ + return chrCopyNumber_[index].getFilteredMAFat(i); +} + +void GenomeCopyNumber::fixExpectedRatioAndMAF(GenomeGMM& gmm, const std::vector& ratio, const std::vector& sm_maf, int ploidy, float purity) +{ + gmm.calculateExpectedRatioAndMAF(ploidy, purity); + gmm.shiftMAF(ratio, sm_maf, ploidy, purity); +} + +double GenomeCopyNumber::processGMM(std::string const& outFile, int tau, float alpha, +bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty) +{ + map::iterator it; + std::vector genome_ratio_full; + std::vector genome_ratio_smoothed_full; + std::vector genome_maf_smoothed_full; + for (it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) { + string::size_type pos = 0; + string chrNumber = (*it).first; + if ( ( pos = chrNumber.find("chr", pos)) != string::npos ) { + chrNumber.replace( pos, 3, "" ); + } + int index = findIndex(chrNumber); + if (index != NA) { + int length_filtered = chrCopyNumber_[index].getFilteredLength(); + for (int i = 0; i < length_filtered; i++) { + float fratio = getFilteredRatio(index, i); + float fmaf = getFilteredMAF(index, i); + genome_ratio_smoothed_full.push_back(fratio); + genome_maf_smoothed_full.push_back(fmaf); + } + ChrCopyNumber cnr = chrCopyNumber_[index]; + int length = cnr.getSNPLength(); + for (int i = 0; i < length; i++) { + float r = chrCopyNumber_[index].getRatioPerSNPat(i); + if ((cnr.getRescaledRatioAtBin(i) != -1) && (cnr.getRescaledRatioAtBin(i) < 3) && (cnr.getSmoothedMAFat(i) != -1)) { + genome_ratio_full.push_back(r); + } + } + } + } + + + GenomeGMM sampleGMM; + auto start = std::chrono::high_resolution_clock::now(); + fixExpectedRatioAndMAF(sampleGMM, genome_ratio_full, genome_maf_smoothed_full, tau, alpha); + sampleGMM.printExpectedRatioAndMAF(outFile, tau, alpha); + auto stop = std::chrono::high_resolution_clock::now(); + auto duration = std::chrono::duration_cast(stop - start); +#pragma omp critical + cout << "fixExpectedRatioAndMAF with tau/alpha:\t" << tau << " / " << alpha << "\ttook " << duration.count() << " s" << endl; + + std::vector genome_ratio_smoothed; + std::vector genome_maf_smoothed; + if (take_subsample_flag){ + std::vector genome_ratio_smoothed_trunc; + std::vector genome_maf_smoothed_trunc; + for (int i = 0; i < genome_ratio_smoothed_full.size(); i+=take_each_nth_element_for_gmm_fit) + { + genome_ratio_smoothed_trunc.push_back(genome_ratio_smoothed_full.at(i)); + genome_maf_smoothed_trunc.push_back(genome_maf_smoothed_full.at(i)); + } + genome_ratio_smoothed = genome_ratio_smoothed_trunc; + genome_maf_smoothed = genome_maf_smoothed_trunc; + } else { + genome_ratio_smoothed = genome_ratio_smoothed_full; + genome_maf_smoothed = genome_maf_smoothed_full; + } + + std::cout << "take_subsample_flag:\t" << take_subsample_flag << std::endl; + std::cout << "Size of genome_maf_smoothed for fitting:\t" << genome_maf_smoothed.size() << "\t\% of full:\t" << (float)genome_maf_smoothed.size() / genome_maf_smoothed_full.size()<< std::endl; + + start = std::chrono::high_resolution_clock::now(); + double bestL = sampleGMM.fitPredict(tau, alpha, genome_ratio_smoothed, genome_maf_smoothed); + stop = std::chrono::high_resolution_clock::now(); + duration = std::chrono::duration_cast(stop - start); +#pragma omp critical + cout << "fitPredict with tau/alpha:\t" << tau << " / " << alpha << "\ttook " << duration.count() << " s" << endl; + + double penalty; + if (usePenalty){ + std::vector weights; + std::vector covs; + auto mixtures = sampleGMM.getMixtures(); + std::vector mus; + for(auto m:mixtures){ + weights.push_back(m.getMixtureComponentWeight()); + covs.push_back(m.getMixtureComponentCov()); + mus.push_back(m.getMixtureComponentMu()); + } + int N = genome_maf_smoothed.size(); + Eigen::MatrixXd mus2(mus.size(), mus.at(0).size()); + for (int i = 0; i < mus.size(); ++i) { + mus2.row(i) = mus.at(i); + } + penalty = compute_penalty(weights, covs, mus2, N); + } else { + penalty = 0; + } + cout << "PENALTY with tau/alpha:\t" << tau << " / " << alpha << "\t-\t" << penalty << endl; + double finalScore = (bestL - penalty); + return finalScore; } + + +template +bool contains(vector vec, const T & elem) +{ + bool result = false; + if( find(vec.begin(), vec.end(), elem) != vec.end() ) + { + result = true; + } + return result; +} + + +float GenomeCopyNumber::compute_penalty(const std::vector& weights, const std::vector& covs, + Eigen::MatrixXd mu, int N, + float threshold_empty, + float threshold_noise, + int C +) { + std::vector empty_clusters; + std::vector noise_clusters; + std::vector non_empty_clusters; + #pragma omp critical +{ + for (int i = 0; i < weights.size(); i++) { + auto weight = weights[i]; + if (weight <= threshold_empty) {std::cout << "/* weight:\t" << weight << std::endl; empty_clusters.push_back(i);} + else {non_empty_clusters.push_back(i);} + } + + for (int i = 0; i < covs.size(); i++) { + auto cov = covs.at(i)(0, 0); + if (cov > threshold_noise) {std::cout << "/* cov:\t" << cov << std::endl; noise_clusters.push_back(i);} + } + } + auto inside = + (mu(empty_clusters, 0).array() <= mu(non_empty_clusters, 0).maxCoeff()) || + (mu(empty_clusters, 1).array() <= mu(non_empty_clusters, 1).maxCoeff()); + for (int i = 0; i < empty_clusters.size(); ++i) { + if (!inside[i]) + empty_clusters.erase(empty_clusters.begin() + i); + } + + std::vector unwanted_clusters; + for(int cluster_idx:noise_clusters){ + if(!contains(unwanted_clusters, cluster_idx)){ + unwanted_clusters.push_back(cluster_idx); + } + } + for(int cluster_idx:empty_clusters){ + if(!contains(unwanted_clusters, cluster_idx)){ + unwanted_clusters.push_back(cluster_idx); + } + } + + int n_clusters = weights.size(); + int I = n_clusters - unwanted_clusters.size(); + float penalty = C*I*log(N); + + std::cout << "PENALTY info:" << std::endl; + std::cout << "n_clusters:\t" << n_clusters << std::endl; + std::cout << "threshold_noise:\t" << threshold_noise << std::endl; + std::cout << "C:\t" << C << std::endl; + std::cout << "empty_clusters:\t" << empty_clusters.size() << std::endl; + std::cout << "noise_clusters:\t" << noise_clusters.size() << std::endl; + std::cout << "unwanted_clusters:\t" << unwanted_clusters.size() << std::endl; + + return penalty; +} + + +double getRandomNum(){ + return (double) rand()/RAND_MAX; +} + +// Print the file with the likelihoods +void GenomeCopyNumber::printGMMFinalLikelihoods(std::string const& outFile, const std::vector>& ploidy_purity_pairs, const std::vector likelihoods, const std::vector number_of_iterations) +{ + std::ofstream file (outFile.c_str()); + file << "Ploidy\tPurity\tFinalLikelihood\tNumberOfIterations"; + file << "\n"; + int n = likelihoods.size(); + if (n != ploidy_purity_pairs.size()) { + std::cerr << "Error: list of ploidy-purity pairs and list of likelihoods should have the same size!" << std::endl; + } + for (int i = 0; i < n; i++) { + file << ploidy_purity_pairs[i].first << "\t" << ploidy_purity_pairs[i].second << "\t" << likelihoods[i] << "\t" << number_of_iterations[i] << "\n"; + } + file.close(); +} + diff --git a/src/GenomeCopyNumber.h b/src/GenomeCopyNumber.h index 2a8540a..c12ba15 100644 --- a/src/GenomeCopyNumber.h +++ b/src/GenomeCopyNumber.h @@ -13,6 +13,7 @@ #include #include #include "SVfinder.h" +#include #include "myFunc.h" #include "ChrCopyNumber.h" @@ -20,6 +21,10 @@ #include "chisquaredistr.h" //to calculate chisquare distribution #include "EntryCNV.h" #include "SNPinGenome.h" +#include "GenomeGMM.h" +#include "bayes_opt.h" +#include + class GenomeCopyNumber { @@ -75,9 +80,9 @@ class GenomeCopyNumber float evaluateContamination(); float evaluateContaminationwithLR(); - void printRatio(std::string const& outFile, bool ifBedGraphOutPut, bool printNA); - void printRatio(std::string const& chr, std::string const& outFile, bool printNA); - void printRatio(std::string const& chr, std::ofstream & file, bool printNA); + void printRatio(std::string const& outFile, bool ifBedGraphOutPut, bool printNA, bool has_smoothed_profile = false, bool has_MAF = false); + void printRatio(std::string const& chr, std::string const& outFile, bool printNA, bool has_smoothed_profile, bool has_MAF); + void printRatio(std::string const& chr, std::ofstream & file, bool printNA, bool has_smoothed_profile, bool has_MAF); void printRatioBedGraph(std::string const& chr, std::ofstream & file, std::string const& typeCNA); void printPloidy(std::string const& outFile) ; void printPloidy(std::ofstream & file); @@ -124,6 +129,9 @@ class GenomeCopyNumber bool ifHasBAF(); void setSex(std::string sex); void setSeekSubclones(bool seekSubclones); + void setDataSubsamplingRateInPuritySearch(int dataSubsamplingRateInPuritySearch); + void setDataSubsamplingRateInPloidyEvaluation(int dataSubsamplingRateInPloidyEvaluation); + void setDoRescaleRatio(bool doRescaleRatio); int findWinNumber(int position, std::string myName, std::string const& matefile); void setWESanalysis(bool WESgiven); @@ -131,8 +139,26 @@ class GenomeCopyNumber void setIfLogged(bool); double Percentage_GenomeExplained(int &); - long double calculateRSS(int ploidy); + long double calculateRSS(int ploidy); bool isMappUsed(); + int getDataSubsamplingRateInPuritySearch(); + int getDataSubsamplingRateInPloidyEvaluation(); + + // Added by Gara + float findMaximumPeak(std::vector total_ratio); + void rescaleRatio(); + void preprocessing(SNPinGenome& snpingenome); + // Print preprocessing outputs + void printRatioAfterPreprocessing(std::string const& outFile); + // Get ratio and MAF vectors that span on the whole genome, instead of a single chromosome + float getFilteredRatio(int index, int i); + float getFilteredMAF(int index, int i); + // For a given pair of ploidy tau and purity alpha, the means of ratio and MAF are fixed + void fixExpectedRatioAndMAF(GenomeGMM& gmm, const std::vector& ratio, const std::vector& sm_maf, int ploidy, float purity); + // Fit the GMM + double processGMM(std::string const& outFile, int tau, float alpha, bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty = true); + + void printGMMFinalLikelihoods(std::string const& outFile, const std::vector>& ploidy_purity_pairs, const std::vector likelihoods, const std::vector number_of_iterations); private: @@ -145,6 +171,9 @@ class GenomeCopyNumber bool isRatioLogged_; void fillMyHash(std::string const& mateFileName , std::string const& inputFormat, std::string const& matesOrientation, int windowSize, int step, std::string targetBed = ""); + int dataSubsamplingRateInPuritySearch; + int dataSubsamplingRateInPloidyEvaluation; + bool doRescaleRatio; int windowSize_; int step_; long totalNumberOfPairs_; @@ -165,6 +194,16 @@ class GenomeCopyNumber std::string pathToSambamba_; std::string pathToReference_; std::string SambambaThreads_; + + float eval_objective(GenomeGMM sampleGMM, int tau, float alpha, std::vector& genome_ratio_smoothed, + std::vector& genome_maf_smoothed); + + float + compute_penalty(const std::vector &weights, const std::vector &covs, Eigen::MatrixXd mu, + int N, + float threshold_empty = 5e-3, + float threshold_noise = 0.1, + int C = 7500); }; #endif diff --git a/src/GenomeGMM.cpp b/src/GenomeGMM.cpp new file mode 100644 index 0000000..c8ef4ff --- /dev/null +++ b/src/GenomeGMM.cpp @@ -0,0 +1,463 @@ +// +// Created by Garance Jaques on 31.05.22. +// + +#include +#include +#include +#include "GenomeGMM.h" +#include "myFunc.h" +#include "cumNormalDistr.h" + +#include "ConfigFile.h" + +GenomeGMM::GenomeGMM() { + shifted_MAF_ = false; + finalL_ = 0.0; + number_of_iterations_ = 0; +} +GenomeGMM::~GenomeGMM() {} + +float GenomeGMM::estimateSigmaAB(const std::vector& ratio, const std::vector& maf, int ploidy, float purity) +{ + std::cout << "..Estimate sigma of cluster AB" << std::endl; + float estimated_sigma = -1; + float ratio1 = (purity + 2*(1 - purity))/(purity*ploidy + 2*(1 - purity)); + float ratio2 = 2/(purity*ploidy + 2*(1 - purity)); + float ratio3 = (purity*3 + 2*(1 - purity))/(purity*ploidy + 2*(1 - purity)); + if (ratio.size() != maf.size()) { + std::cerr << "Error: ratio and MAF vectors should be of the same size." << std::endl; + } + std::vector maf_diploid; + for (unsigned int i = 0; i < ratio.size(); i++) { + if((ratio[i] >= ((ratio1 + ratio2)/2)) & (ratio[i] <= ((ratio2 + ratio3)/2))) { + float maf_val = maf[i]; + maf_diploid.push_back(maf_val); + } + } + if (!maf_diploid.empty()) { + float max_maf = *std::max_element(maf_diploid.begin(), maf_diploid.end()); + std::cout << "Max element of MAF diploid 2: " << max_maf << std::endl; + int n = ceil((max_maf+0.001-0.500)/0.001); + std::vector bins(n); + float x = 0.499; + std::generate(bins.begin(), bins.end(), [&]{return x+=0.001;}); + std::vector counts = makeHistogramOfCounts(maf_diploid, bins); + std::map peaks = findPeaks(counts, 2, 50, 20); + if (peaks.size() != 0) { + // Find the peak that is closest to 0.5 + float maf_empirical_mean = max_maf + 0.001; + int peak_pos = 0; + float peak_freq = max_maf + 0.001; + float diff = abs(maf_empirical_mean - 0.500); + for (std::map::iterator it = peaks.begin(); it != peaks.end(); ++it) { + peak_pos = it->first; + peak_freq = bins[peak_pos]; + if (abs(peak_freq - 0.5) < diff) { + diff = abs(peak_freq - 0.500); + maf_empirical_mean = peak_freq; + } + } + std::cout << "MAF empirical mean 2: " << maf_empirical_mean << std::endl; + if (maf_empirical_mean <= 0.6) { + estimated_sigma = (maf_empirical_mean - 0.5)*std::pow(2*PI_, 0.5)*0.5; + } + } + } + std::cout << "Estimated sigma: " << estimated_sigma << std::endl; + return estimated_sigma; +} + +float GenomeGMM::estimateSigmaAABB(const std::vector& ratio, const std::vector& maf, int ploidy, float purity) +{ + std::cout << "..Estimate sigma using cluster AABB" << std::endl; + float estimated_sigma = -1; + float ratio3 = (purity*3 + 2*(1 - purity))/(purity*ploidy + 2*(1 - purity)); + float ratio4 = (2 + 2*purity)/(purity*ploidy + 2*(1 - purity)); + float ratio5 = (purity*5 + 2*(1 - purity))/(purity*ploidy + 2*(1 - purity)); + if (ratio.size() != maf.size()) { + std::cerr << "Error: ratio and MAF vectors should be of the same size." << std::endl; + } + std::vector maf_diploid; + for (unsigned int i = 0; i < ratio.size(); i++) { + if((ratio[i] >= ((ratio3 + ratio4)/2)) & (ratio[i] <= ((ratio4 + ratio5)/2))) { + float maf_val = maf[i]; + maf_diploid.push_back(maf_val); + } + } + if (!maf_diploid.empty()) { + float max_maf = *std::max_element(maf_diploid.begin(), maf_diploid.end()); + std::cout << "Max element MAF diploid 4: " << max_maf << std::endl; + int n = ceil((max_maf+0.001-0.500)/0.001); + std::vector bins(n); + float x = 0.500; + std::generate(bins.begin(), bins.end(), [&]{return x+=0.001;}); + std::vector counts = makeHistogramOfCounts(maf_diploid, bins); + std::map peaks = findPeaks(counts, 2, 50, 20); + if (peaks.size() != 0) { + // Find the peak that is closest to 0.5 + float maf_empirical_mean = max_maf + 0.001; + int peak_pos = 0; + float peak_freq = maf_empirical_mean; + float diff = abs(maf_empirical_mean - 0.500); + for (std::map::iterator it = peaks.begin(); it != peaks.end(); ++it) { + peak_pos = it->first; + peak_freq = bins[peak_pos]; + if (abs(peak_freq - 0.5) < diff) { + diff = abs(peak_freq - 0.500); + maf_empirical_mean = peak_freq; + } + } + std::cout << "MAF empirical mean 4: " << maf_empirical_mean << std::endl; + if (maf_empirical_mean <= 0.6) { + estimated_sigma = (maf_empirical_mean - 0.5)*pow(2*PI_, 0.5)*0.5; + } + } + } + std::cout << "Estimated sigma: " << estimated_sigma << std::endl; + return estimated_sigma; +} + +float GenomeGMM::calculateSigma(int ploidy, float purity, int i, float sigma2, float sigma4) +{ + float threshold = 1.0/3.0; + if (sigma2 != -1) { + float sigma = sigma2*pow(1/expected_ratio_[i], 0.5) * pow(expected_maf_[i]*(1 - expected_maf_[i]), 0.5)/0.5; + if (sigma < threshold) { + return sigma; + } else { + std::cerr << "Warning: the estimated sigma is very high and is thus set to 1/3" << std::endl; + sigma = threshold; + return sigma; + } + } else if (sigma4 != -1) { + float sigma = sigma4*pow(1/expected_ratio_[i], 0.5) * pow(expected_maf_[i]*(1-expected_maf_[i]), 0.5)/0.5; + if (sigma < threshold) { + return sigma; + } else { + std::cerr << "Warning: the estimated sigma is very high and is thus set to 1/3" << std::endl; + sigma = threshold; + return sigma; + } + } else { + std::cerr << "Error: either sigma2 or sigma4 should be passed as non-default arguments!" << std::endl; + } +} + +void GenomeGMM::correctMAF(std::vector sigma) +{ + std::cout << "..Correct MAF expected values" << std::endl; + shifted_expected_maf_.resize(length_expectation_); + float exp_BAF1, exp_BAF2 = 0; + float pdf1, pdf2, cdf1, cdf2, term1, term2 = 0; + for (int i = 0; i < length_expectation_; i++) { + exp_BAF1 = expected_maf_[i]; + exp_BAF2 = 1 - exp_BAF1; + pdf1 = NormalDistributionDensity(0.5, exp_BAF1, sigma[i]); + pdf2 = NormalDistributionDensity(0.5, exp_BAF2, sigma[i]); + cdf1 = calculateNormalCDF(0.5, exp_BAF1, sigma[i]); + cdf2 = calculateNormalCDF(0.5, exp_BAF2, sigma[i]); + term1 = exp_BAF1 * (1 - cdf1) + pow(sigma[i], 2) * pdf1; + term2 = exp_BAF2 * (1 - cdf2) + pow(sigma[i], 2) * pdf2; + shifted_expected_maf_[i] = term1 + term2; + std::cout << "Shifted MAF: " << shifted_expected_maf_[i] << " and corresponding sigma: " << sigma[i] << std::endl; + } +} + +void GenomeGMM::shiftMAF(const std::vector& ratio, const std::vector& maf_smoothed, int ploidy, float purity) +{ + std::cout << "..Shift MAF centers" << std::endl; + std::vector estimated_sigma(length_expectation_); + + float sigma2 = estimateSigmaAB(ratio, maf_smoothed, ploidy, purity); + if ((sigma2 != -1) & (ploidy < 4)) { + for (int i = 0; i < length_expectation_; i++) { + estimated_sigma[i] = calculateSigma(ploidy, purity, i, sigma2, -1); + } + correctMAF(estimated_sigma); + shifted_MAF_ = true; + } else { + float sigma4 = estimateSigmaAABB(ratio, maf_smoothed, ploidy, purity); + if (sigma4 != -1) { + for (int i = 0; i < length_expectation_; i++) { + estimated_sigma[i] = calculateSigma(ploidy, purity, i, -1, sigma4); + } + correctMAF(estimated_sigma); + shifted_MAF_ = true; + } else { + std::cerr << "Warning! Cluster centers were not corrected for shifting" << std::endl; + shifted_expected_maf_ = expected_maf_; + } + } +} + +void GenomeGMM::calculateExpectedRatioAndMAF(int ploidy, float purity) +{ + std::cout << "..Calculate expected ratio and expected MAF" << std::endl; + int max_copy_number = 0; + switch(ploidy) { + case 1: + max_copy_number = 5; + break; + case 2: + max_copy_number = 7; + break; + case 3: + max_copy_number = 10; + break; + case 4: + max_copy_number = 12; + break; + default: + max_copy_number = 15; + } + std::vector Q; + std::vector Qh; + for(int i = 0; i <= max_copy_number; i++) { + for(int j = ceil((float)i/(float)2); j <= i; j++) { + Q.push_back(i); + Qh.push_back(j); + } + } + int n = Q.size(); + length_expectation_ = n; + expected_ratio_.reserve(n); + expected_maf_.reserve(n); + float normalFraction = 2*(1 - purity); + for(int i = 0; i < n; i++) { + expected_ratio_.push_back((Q[i]*purity + normalFraction)/(purity*ploidy + normalFraction + 1e-8)); + expected_maf_.push_back((purity*Qh[i] + 1 - purity)/(purity*Q[i] + normalFraction + 1e-8)); + } + K_ = expected_ratio_.size(); +} + + +Eigen::VectorXd GenomeGMM::transformVectorToMatrix(const std::vector& v) +{ + const double* cpv = v.data(); + Eigen::VectorXd vxd = Eigen::VectorXd::Map(cpv, v.size()); + return vxd; +} + +void GenomeGMM::initialiseGMMParameters(int n_init, int max_iter, double tol, double reg_cov, double noise, bool b, double lbr, double ubr, double lbm, double ubm) +{ + setNinit(n_init); + setMaxIter(max_iter); + setTolerance(tol); + setRegCovar(reg_cov); + setNoise(noise); + setBound(b); + setBoundsRatio(lbr, ubr); + setBoundsMAF(lbm, ubm); +} + +Eigen::Matrix2d GenomeGMM::initialiseCovariance() { + Eigen::Matrix2d cov; + cov << 0.005, 0.0, 0.0, 0.01; + return cov; +} + +double GenomeGMM::initialiseWeight() { + return (double)1/(double)K_; +} + +std::vector GenomeGMM::calculateMarginalResponsabilities(int n) +{ + std::vector marginal_responsabilities; + marginal_responsabilities.resize(n); + for (int i = 0; i < n; i++) { + double marginal_responsability = 0; + for (int k = 0; k < K_; k++) { + marginal_responsability += exp(log(mixture_[k].getMixtureComponentWeight()) + mixture_[k].getMixtureComponentLikelihoodAt(i)); + } + marginal_responsabilities[i] = log(marginal_responsability); + } + return marginal_responsabilities; +} + +double GenomeGMM::computeLoss(int n) +{ + double likelihood = 0.0; + for (int i = 0; i < n; i++) { + double marg_likelihood = 0.0; + for (int k = 0; k < K_; k++) { + double component_weight = mixture_[k].getMixtureComponentWeight(); + double l = exp(log(component_weight) + mixture_[k].getMixtureComponentLikelihoodAt(i)); + marg_likelihood += l; + } + double log_marg = log(marg_likelihood); + likelihood += log_marg; + } + return likelihood; +} + +double GenomeGMM::fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf) +{ + // TMP + #ifdef CLUSTER + ConfigFile cf("/cluster/home/kzaitse/custom_configs/freec_configs/meta-config.txt"); + #else + ConfigFile cf("/local/home/kzaitse/lab/custom_configs/freec_configs/meta-config.txt"); + #endif // !CLUSTER + int maxIter = (int)cf.Value("gmm", "maxIter", 1); + initialiseGMMParameters(1, maxIter, 2000, 1.0e-7, 1, false, 0.0, 0.01, 0.0, 0.015); + + if (noise_ == 1) { + expected_ratio_.push_back(1.0); + expected_maf_.push_back(0.95); + shifted_expected_maf_.push_back(0.95); + K_ = expected_ratio_.size(); + } + mixture_.resize(K_); + int N = ratio.size(); + + // Transform std::vectors in Eigen::vectors for matrix operations + std::vector d_ratio(ratio.begin(), ratio.end()); + std::vector d_maf(maf.begin(), maf.end()); + Eigen::VectorXd e_ratio = transformVectorToMatrix(d_ratio); + Eigen::VectorXd e_maf = transformVectorToMatrix(d_maf); + + // Initialise all mixture components + Eigen::Matrix2d cov = initialiseCovariance(); + double w = initialiseWeight(); + for (int k = 0; k < K_; k++) { + std::vector mu = {expected_ratio_[k], shifted_expected_maf_[k]}; + Eigen::VectorXd ex_mu; + ex_mu = transformVectorToMatrix(mu); + Eigen::Vector2d e_mu; + if (ex_mu.size() == 2) { + e_mu << ex_mu; + } else { + std::cerr << "Error: mu needs to be of size 2!" << std::endl; + } + MixtureComponent m(e_ratio, e_maf, e_mu, w, cov, N); + mixture_[k] = m; + } + + // Initialise variables used in the EM algorithm + std::vector marginal_responsabilities(N); + double currentL = 0.0; + double previousL = 0.0; + + // EM algorithm + int iter = 0; + double diff = std::numeric_limits::infinity(); + std::cout << "Begin of EM algorithm" << std::endl; + while((iter < max_iter_) & (abs(diff) > tolerance_)) { + std::cout << tau << "/" << alpha << ":\tIteration " << iter << std::endl; + // E-step + std::cout << "..Calculate sample likelihood" << std::endl; + for (int k = 0; k < K_; ++k) { + mixture_[k].calculateSampleLikelihoods(N); + } + marginal_responsabilities = calculateMarginalResponsabilities(N); + for (int k = 0; k < K_; k++) { + mixture_[k].calculateComponentResponsabilities(marginal_responsabilities); + mixture_[k].updateCovarianceAndWeight(bound_, lower_bound_ratio_, upper_bound_ratio_, lower_bound_maf_, upper_bound_maf_); + mixture_[k].calculateSampleLikelihoods(N); + } + previousL = currentL; + currentL = computeLoss(N); + std::cout << tau << "/" << alpha << ":\tCurrent likelihood: " << currentL << std::endl; + diff = (currentL - previousL); + + if (diff > 1e8){ + std::cout << "Clipping difference between current and previous likelihood to 1e8" << diff << std::endl; + diff = 1e8; + } else if (diff < -1e8){ + std::cout << "Clipping difference between current and previous likelihood to -1e8" << diff << std::endl; + diff = -1e8; + } else{ + std::cout << tau << "/" << alpha << ":\tDifference between current and previous likelihood: " << diff << std::endl; + } + + iter += 1; + if (iter >= max_iter_) { + std::cout << "The algorithm stopped because it reached the maximum number of iterations " << max_iter_ << std::endl; + } else if (abs(diff) <= tolerance_) { + std::cout << "The algorithm stopped because the difference between the current and the previous likelihood is below the given tolerance " << tolerance_ << std::endl; + } + } + finalL_ = currentL; + number_of_iterations_ = iter; + return finalL_; +} + + +void GenomeGMM::printExpectedRatioAndMAF(std::string const& outFile, int ploidy, float purity) { + std::string myName = outFile + "_cluster-centers_ploidy" + std::to_string(ploidy) + "_purity" + std::to_string(purity) + ".txt"; + std::ofstream file (myName.c_str()); + + file << "Cluster centers coordinates for ploidy " << ploidy << " and purity " << purity; + file << "\n" << "\n" << "\n"; + file << "ExpectedRatio\tExpectedMAF"; + if (shifted_MAF_) { + file << "\tShiftedExpectedMAF"; + } + file << "\n"; + + for (int i = 0; i < expected_ratio_.size(); i++) { + file << expected_ratio_[i] << "\t" << expected_maf_[i]; + if (shifted_MAF_) { + file << "\t" << shifted_expected_maf_[i]; + } + file << "\n"; + } + file.close(); + std::cout << "Wrote CLUSTER CENTERS to file:\t" << myName << std::endl; +} + +double GenomeGMM::getFinalL() +{ + return finalL_; +} + +int GenomeGMM::getNumberOfIterations() +{ + return number_of_iterations_; +} + +void GenomeGMM::setNinit(int n) +{ + n_init_ = n; +} + +void GenomeGMM::setMaxIter(int m) +{ + max_iter_ = m; +} + +void GenomeGMM::setTolerance(double t) +{ + tolerance_ = t; +} +void GenomeGMM::setRegCovar(double c) +{ + reg_covar_ = c; +} + +void GenomeGMM::setNoise(double n) +{ + noise_ = n; +} + +void GenomeGMM::setBound(bool b) +{ + bound_ = b; +} + +void GenomeGMM::setBoundsRatio(double l, double u) +{ + lower_bound_ratio_ = l; + upper_bound_ratio_ = u; +} + +void GenomeGMM::setBoundsMAF(double l, double u) +{ + lower_bound_maf_ = l; + upper_bound_maf_ = u; +} + +std::vector GenomeGMM::getMixtures() { + return mixture_; +} diff --git a/src/GenomeGMM.h b/src/GenomeGMM.h new file mode 100644 index 0000000..c459f27 --- /dev/null +++ b/src/GenomeGMM.h @@ -0,0 +1,87 @@ +// +// Created by Garance Jaques on 31.05.22. +// + +#ifndef SRC_GENOMEGMM_H +#define SRC_GENOMEGMM_H + +#include +#include +#include +#include "ap.h" +#include "MixtureComponent.h" + + +class GenomeGMM { +public: + GenomeGMM(); + ~GenomeGMM(); + + // Methods for shifting expected MAF + float estimateSigmaAB(const std::vector& ratio, const std::vector& maf, int ploidy, float purity); + float estimateSigmaAABB(const std::vector& ratio, const std::vector& maf, int ploidy, float purity); + float calculateSigma(int ploidy, float purity, int i, float sigma2 = -1, float sigma4 = -1); + Eigen::MatrixXd subclonalClusters(float s, const std::vector &ratio, const std::vector &maf, float alpha, float tau); + void correctMAF(std::vector sigma); + void shiftMAF(const std::vector& ratio, const std::vector& maf_smoothed, int ploidy, float purity); + // For a given pair of ploidy and purity, the means of ratio and MAF are fixed + void calculateExpectedRatioAndMAF(int ploidy, float purity); + // Print the cluster centres + void printExpectedRatioAndMAF(std::string const& outFile, int ploidy, float purity); + + // Helper function that transforms std::vector into Eigen::Vector so that I can use matrices + // in the GMM fitting part without having to transform them every time + Eigen::VectorXd transformVectorToMatrix(const std::vector& v); + + // Methods for model fitting + void initialiseGMMParameters(int n_init = 1, int max_iter = 600, double tol = 5.0e-3, double reg_cov = 1.0e-7, double noise = 1, bool b = false, double lbr = 0.0, double ubr = 0.01, double lbm = 0.0, double ubm = 0.015); + Eigen::Matrix2d initialiseCovariance(); + double initialiseWeight(); + std::vector calculateMarginalResponsabilities(int n); + double computeLoss(int n); + double fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf); + + + // Get methods + std::vector getMixtures(); + double getFinalL(); + int getNumberOfIterations(); + + // Set methods + void setNinit(int n); + void setMaxIter(int m); + void setTolerance(double t); + void setRegCovar(double c); + void setNoise(double n); + void setBound(bool b); + void setBoundsRatio(double l, double u); + void setBoundsMAF(double l, double u); + +private: + int length_expectation_; + std::vector expected_ratio_; + std::vector expected_maf_; + std::vector shifted_expected_maf_; + bool shifted_MAF_; + int K_; + double finalL_; + int number_of_iterations_; + + // GMM parameters + int n_init_; + int max_iter_; + double tolerance_; + double reg_covar_; + double noise_; + bool bound_; + double lower_bound_ratio_; + double upper_bound_ratio_; + double lower_bound_maf_; + double upper_bound_maf_; + + // GMM + std::vector mixture_; +}; + + +#endif //SRC_GENOMEGMM_H diff --git a/src/Makefile.freec b/src/Makefile.freec index 3220a91..1b01a6e 100644 --- a/src/Makefile.freec +++ b/src/Makefile.freec @@ -17,17 +17,17 @@ ifeq (aarch64,$(shell uname -m)) M64_FLAG = endif +INCLUDE = -I./include/ +CXXFLAGS = $(CXXOPT) $(EXTRA_CXXFLAGS) $(INCLUDE) -Wall $(M64_FLAG) -CXXFLAGS = $(CXXOPT) $(EXTRA_CXXFLAGS) -Wall $(M64_FLAG) - -MAKEDEPEND = gcc -M $(EXTRA_CXXFLAGS) +MAKEDEPEND = gcc -M $(EXTRA_CXXFLAGS) $(INCLUDE) PROG = freec all: $(PROG) -$(PROG): main.o ConfigFile.o Chameleon.o GenomeDensity.o Help.o myFunc.o KernelVector.o ChrDensity.o ChrCopyNumber.o GenomeCopyNumber.o chisquaredistr.o ap.o igammaf.o gammafunc.o normaldistr.o ablasf.o ablas.o ortfac.o sblas.o rotations.o reflections.o linreg.o hblas.o descriptivestatistics.o creflections.o blas.o bdsvd.o svd.o ialglib.o EntryCNV.o SNPinGenome.o SNPatChr.o SNPposition.o binomialdistr.o ibetaf.o ThreadPool.o BAFpileup.o SeekSubclones.o +$(PROG): main.o ConfigFile.o Chameleon.o GenomeDensity.o Help.o myFunc.o KernelVector.o ChrDensity.o ChrCopyNumber.o GenomeCopyNumber.o chisquaredistr.o ap.o igammaf.o gammafunc.o normaldistr.o ablasf.o ablas.o ortfac.o sblas.o rotations.o reflections.o linreg.o hblas.o descriptivestatistics.o creflections.o blas.o bdsvd.o svd.o ialglib.o EntryCNV.o SNPinGenome.o SNPatChr.o SNPposition.o binomialdistr.o ibetaf.o ThreadPool.o BAFpileup.o SeekSubclones.o GenomeGMM.o gaussianKernel.o cumNormalDistr.o MixtureComponent.o g++ $(M64_FLAG) $(CXXOPT) -o $(PROG) $+ $(EXTRA_LDFLAGS) init: diff --git a/src/MixtureComponent.cpp b/src/MixtureComponent.cpp new file mode 100644 index 0000000..e9da188 --- /dev/null +++ b/src/MixtureComponent.cpp @@ -0,0 +1,142 @@ +// +// Created by Garance Jaques on 17.06.22. +// + +#include "MixtureComponent.h" +#include + +MixtureComponent::MixtureComponent() {} +MixtureComponent::MixtureComponent(const Eigen::VectorXd& ratio, const Eigen::VectorXd& maf, const Eigen::Vector2d& mu, float w, const Eigen::Matrix2d& cov, int N) { + mu_ = mu; + weight_ = w; + covariance_ = cov; + shift_.resize(ratio.size(), 2); + shift_ << computeShift(ratio, maf); + responsabilities_.resize(N); +} +MixtureComponent::~MixtureComponent() {} + + +// EM methods +Eigen::MatrixXd MixtureComponent::computeShift(const Eigen::VectorXd& ratio, const Eigen::VectorXd& maf) +{ + int n = ratio.size(); + Eigen::MatrixXd shift(n, 2); + double r, m = 0.0; + if (n != maf.size()) { + std::cerr << "Error: ratio and MAF vectors must have the same size" << std::endl; + } else { + for (int i = 0; i < n; i++) { + r = ratio(i) - mu_(0); + m = maf(i) - mu_(1); + shift.row(i) << r, m; + } + } + return shift; +} + +void MixtureComponent::calculateSampleLikelihoods(int n) { + int D = 2; + likelihoods_.resize(n); + double det = covariance_(0,0)*covariance_(1,1); + double denom = std::pow(std::sqrt(2*PI_), -D/2.0) * std::pow(det, -0.5); + double inv11 = covariance_(1,1)/det; + double inv22 = covariance_(0,0)/det; + Eigen::Matrix2d inverse; + inverse << inv11, 0.0, 0.0, inv22; + for (int i = 0; i < n; i++) { + Eigen::RowVector2d shift; + shift << shift_.row(i); + double exp_term = -0.5 * shift * inverse * shift.transpose(); + likelihoods_[i] = log(denom) + exp_term; + } +} + +void MixtureComponent::calculateComponentResponsabilities(const std::vector& marginal_responsabilities) +{ + int n = marginal_responsabilities.size(); + if (marginal_responsabilities.size() != n) { + std::cerr << "Error: the length of marginal responsabilities vector needs to be the same as the length of the likelihoods vector" << std::endl; + } + for (int i = 0; i < n; i++) { + double joint = log(weight_) + likelihoods_[i]; + responsabilities_[i] = exp(joint - marginal_responsabilities[i]); + } +} + +double MixtureComponent::calculateTotalResponsability() +{ + double total_responsability = 0; + int n = responsabilities_.size(); + for (int i = 0; i < n; i++) { + total_responsability += responsabilities_[i]; + } + //double log_total_responsability = log(total_responsability); + return total_responsability; +} + +void MixtureComponent::updateWeight(double total_resp, int n) +{ + weight_ = (double)total_resp/(double)n; +} + +void MixtureComponent::updateCovariance(bool bound, double total_resp, int n, double lbr, double ubr, double lbm, double ubm) +{ + Eigen::Matrix2d new_cov; + new_cov << 0, 0, 0, 0; + for (int i = 0; i < n; i++) { + Eigen::RowVector2d shift; + shift << shift_.row(i); + new_cov += responsabilities_[i] * shift.transpose() * shift; + } + new_cov = new_cov/total_resp; + covariance_(0,0) = new_cov(0,0); + covariance_(1,1) = new_cov(1,1); + if (bound) { + if (new_cov(0,0) > ubr) { + covariance_(0,0) = ubr; + } else if (new_cov(0,0) < lbr) { + covariance_(0,0) = lbr; + } + if (new_cov(1,1) > ubm) { + covariance_(1,1) = ubm; + } else if (new_cov(1,1) < lbm) { + covariance_(1,1) = lbm; + } + } +} + +void MixtureComponent::updateCovarianceAndWeight(bool bound, double lbr, double ubr, double lbm, double ubm) +{ + int n = responsabilities_.size(); + double total_resp = calculateTotalResponsability(); + updateWeight(total_resp, n); + updateCovariance(bound, total_resp, n, lbr, ubr, lbm, ubm); +} + + +// Get methods +double MixtureComponent::getMixtureComponentWeight() +{ + return weight_; +} +Eigen::Matrix2d MixtureComponent::getMixtureComponentCov() +{ + return covariance_; +} +Eigen::Vector2d MixtureComponent::getMixtureComponentMu() +{ + return mu_; +} + +double MixtureComponent::getMixtureComponentLikelihoodAt(int i) +{ + return likelihoods_[i]; +} + + +// Set methods +void MixtureComponent::setMixtureComponentCovariance(const Eigen::Matrix2d& cov) +{ + covariance_ = cov; +} diff --git a/src/MixtureComponent.h b/src/MixtureComponent.h new file mode 100644 index 0000000..656fbb6 --- /dev/null +++ b/src/MixtureComponent.h @@ -0,0 +1,50 @@ +// +// Created by Garance Jaques on 17.06.22. +// + +#ifndef SRC_MIXTURECOMPONENT_H +#define SRC_MIXTURECOMPONENT_H + +#include +#include +#include +#include "myFunc.h" + +class MixtureComponent { +public: + MixtureComponent(); + MixtureComponent(const Eigen::VectorXd& ratio, const Eigen::VectorXd& maf, const Eigen::Vector2d& mu, float w, const Eigen::Matrix2d& cov, int N); + ~MixtureComponent(); + + // EM methods + Eigen::MatrixXd computeShift(const Eigen::VectorXd& ratio, const Eigen::VectorXd& maf); + void calculateSampleLikelihoods(int n); + void calculateComponentResponsabilities(const std::vector& marginal_responsabilities); + double calculateTotalResponsability(); + void updateWeight(double total_resp, int n); + void updateCovariance(bool bound, double total_resp, int n, double lbr, double ubr, double lbm, double ubm); + void updateCovarianceAndWeight(bool bound, double lbr, double ubr, double lbm, double ubm); + + // Get methods + double getMixtureComponentWeight(); + Eigen::Matrix2d getMixtureComponentCov(); + //std::vector getMixtureComponentLikelihood(); + double getMixtureComponentLikelihoodAt(int i); + + // Set methods + void setMixtureComponentCovariance(const Eigen::Matrix2d& cov); + + Eigen::Vector2d getMixtureComponentMu(); + +private: + Eigen::Vector2d mu_; + Eigen::MatrixXd shift_; + Eigen::Matrix2d covariance_; + double weight_; + std::vector likelihoods_; + std::vector responsabilities_; + +}; + + +#endif //SRC_MIXTURECOMPONENT_H diff --git a/src/SVfinder.h b/src/SVfinder.h index 301b3a4..7dd556c 100644 --- a/src/SVfinder.h +++ b/src/SVfinder.h @@ -35,7 +35,7 @@ #define NA -1 #define FileNameLength 281 //maximal length of file name #define MaxWordLength 281 // LLIB -#define Infinity 1000000000000 +#define INFINITY_ 1000000000000 #define GOODSD 0.5 #define TELO_CENTRO_FLANCS 50000 //#define GOODMAPPABILITY 0.85 diff --git a/src/ThreadPool.h b/src/ThreadPool.h index fa910ce..f253bc2 100644 --- a/src/ThreadPool.h +++ b/src/ThreadPool.h @@ -19,12 +19,12 @@ #include #include //starting from v6.6 for compatibility with Ubuntu -#ifdef _WIN32 +#ifdef _WIN32 //x32 Windows definitions -#include -#else +#include +#else //other platforms -#include +#include #endif class ThreadPool; @@ -101,15 +101,14 @@ class Thread { bool waitFinished() { - #ifdef _WIN32 + #ifdef _WIN32 //x32 Windows definitions Sleep(WAIT_USECONDS); -#else +#else //other platforms usleep(WAIT_USECONDS); #endif - usleep(WAIT_USECONDS); pthread_mutex_lock(&mp); if (state == FINISHED) { pthread_mutex_unlock(&mp); diff --git a/src/bayes_opt.cpp b/src/bayes_opt.cpp new file mode 100644 index 0000000..9752216 --- /dev/null +++ b/src/bayes_opt.cpp @@ -0,0 +1,261 @@ + +#include "bayes_opt.h" +#include "limbo/opt/nlopt_base.hpp" +#include + +#ifndef USE_NLOPT +#warning No NLOpt +#else +#include +#endif + +using namespace limbo; + +struct Params +{ + struct bayes_opt_boptimizer : public defaults::bayes_opt_boptimizer + { + BO_PARAM(int, hp_period, -1); + }; + + struct bayes_opt_bobase : public defaults::bayes_opt_bobase + { + BO_PARAM(int, stats_enabled, true); + BO_PARAM(bool, bounded, true); + BO_DYN_PARAM(std::string, base_dir); + BO_DYN_PARAM(std::string, dir_with_results_prefix); + }; + + struct stop_maxiterations + { + BO_DYN_PARAM(int, iterations); + }; + + struct acqui_ei : public defaults::acqui_ei + { + BO_PARAM(double, jitter, 0.05); + }; + + struct init_randomsampling + { + BO_PARAM(int, samples, 15); + }; + + struct kernel : public defaults::kernel + { + BO_DYN_PARAM(double, noise); + }; + + struct kernel_maternfivehalves : public defaults::kernel_maternfivehalves + { + }; + + struct opt_rprop : public defaults::opt_rprop + { + }; + struct opt_nloptnograd : public defaults::opt_nloptnograd + { + }; +}; + +double my_eval_func(int tau, double alpha, GenomeCopyNumber genomeCopyNumber) +{ + auto start = std::chrono::high_resolution_clock::now(); + double score = genomeCopyNumber.processGMM("/tmp/res-" + std::to_string(tau) + "-" + std::to_string(alpha), tau, alpha, true, genomeCopyNumber.getDataSubsamplingRateInPuritySearch(), false); + auto stop = std::chrono::high_resolution_clock::now(); + auto duration = std::chrono::duration_cast(stop - start); + + if (score > 1e8) + { + std::cout << "Clipping score to 1e8 from: " << score << std::endl; + score = 1e8; + } + else if (score < -1e8 || std::isnan(score)) + { + std::cout << "Clipping score to -1e8 from: " << score << std::endl; + score = -1e8; + } + + std::cout << "processGMM with tau/alpha:\t" << tau << " / " << alpha << "\ttook " << duration.count() << " s" << std::endl; + std::cout << "SCORE with tau/alpha:\t" << tau << " / " << alpha << "\t-\t" << score << std::endl; + return score; +} + +template +struct eval_func +{ + BO_PARAM(size_t, dim_in, 1); + + BO_PARAM(size_t, dim_out, 1); + int tau; + GenomeCopyNumber genomeCopyNumber; + + explicit eval_func(int tau, GenomeCopyNumber genomeCopyNumber) + { + this->tau = tau; + this->genomeCopyNumber = genomeCopyNumber; + } + + Eigen::VectorXd operator()(const Eigen::VectorXd &x) const + { + double alpha = x(0); + double score = my_eval_func(tau, alpha, genomeCopyNumber); + return tools::make_vector(score); + } +}; + +BO_DECLARE_DYN_PARAM(int, Params::stop_maxiterations, iterations); +BO_DECLARE_DYN_PARAM(double, Params::kernel, noise); +BO_DECLARE_DYN_PARAM(std::string, Params::bayes_opt_bobase, base_dir); +BO_DECLARE_DYN_PARAM(std::string, Params::bayes_opt_bobase, dir_with_results_prefix); + +void misc_eval(GenomeCopyNumber genomeCopyNumber, int tau, double alpha) +{ + double score; + score = genomeCopyNumber.processGMM("/tmp/res-trunc-" + std::to_string(tau) + "-" + std::to_string(alpha), tau, alpha, true, genomeCopyNumber.getDataSubsamplingRateInPuritySearch(), false); +#pragma omp critical + std::cout << "TEST SCORE (trunc) with tau/alpha:\t" << tau << " / " << alpha << "\t-\t" << score << std::endl; + score = genomeCopyNumber.processGMM("/tmp/res-full-" + std::to_string(tau) + "-" + std::to_string(alpha), tau, alpha, true, genomeCopyNumber.getDataSubsamplingRateInPloidyEvaluation(), true); +#pragma omp critical + std::cout << "TEST SCORE (full) with tau/alpha:\t" << tau << " / " << alpha << "\t-\t" << score << std::endl; +} + +std::map> findBestPurity(GenomeCopyNumber &sampleCopyNumber, std::vector ploidies, ConfigFile &cf, std::string outputDir) +{ + // TMP + int optimObjectiveCalls = (int)cf.Value("bayesopt", "optimObjectiveCalls", 1); + double kernelNoise = (double)cf.Value("bayesopt", "kernelNoise", 1e-10); + double truePurity = (double)cf.Value("bayesopt", "truePurity", 0.5); + bool runTruePurity = (bool)cf.Value("bayesopt", "runTruePurity", false); + Params::stop_maxiterations::set_iterations(optimObjectiveCalls); + Params::kernel::set_noise(kernelNoise); + Params::bayes_opt_bobase::set_base_dir(outputDir); + + using kernel_t = kernel::MaternFiveHalves; + using gp_t = model::GP; + using acqui_t = acqui::EI; + using acqui_opt_t = opt::NLOptNoGrad; + using init_t = init::RandomSampling; + + using stat_t = boost::fusion::vector, + limbo::stat::AggregatedObservations, + limbo::stat::BestAggregatedObservations, + limbo::stat::BestObservations, + limbo::stat::Samples, + limbo::stat::BestSamples, + limbo::stat::GPLikelihood, + limbo::stat::GPMeanHParams, + limbo::stat::GPPredictionDifferences, + limbo::stat::Observations, + limbo::stat::GPKernelHParams>; + + std::map> best_score_alpha_per_tau; + std::map> best_result; + + if (runTruePurity == true && truePurity != 0.5) + { + int truePloidy = (int)cf.Value("bayesopt", "truePloidy", 0); + if (truePloidy == 0) {std::cout << "truePloidy not provided. Skipping evaluation for the correct pair" << std::endl;} + else { + std::cout << "/* misc_eval(sampleCopyNumber, truePloidy, truePurity); */" << std::endl; + std::cout << "/* misc_eval(sampleCopyNumber, " << truePloidy << ", " << truePurity << "); */" << std::endl; + misc_eval(sampleCopyNumber, truePloidy, truePurity); + } + } + else if (runTruePurity == true) + { + std::cout << "/* runTruePurity == true BUT truePurity is NOT supplied */" << std::endl; + } + + std::vector queryPurities; + std::vector strs; + std::string queryPurities_str = (std::string)cf.Value("bayesopt", "queryPurities", ""); + split(queryPurities_str, ',', strs); + if (strs.size() > 1) + { + std::cout << "QUERY sample purities"; + for (unsigned int i = 0; i < strs.size(); i++) + { + queryPurities.push_back(std::stod(strs[i].c_str())); + std::cout << "/* misc_eval(sampleCopyNumber, " << ploidies.at(0) << ", " << queryPurities.back() << "); */" << std::endl; + misc_eval(sampleCopyNumber, ploidies.at(0), queryPurities.back()); + } + exit(0); + } + else + { + std::cout << "Skipping QUERY sample purities: " << queryPurities_str << std::endl; + } + + bool queryPloidies = (bool)cf.Value("bayesopt", "queryPloidies", false); + if (queryPloidies){ + for (int tau : ploidies){ + best_score_alpha_per_tau.insert({tau, std::make_pair(1, truePurity)}); + } + } else { + omp_lock_t lck; + omp_init_lock(&lck); + + #pragma omp parallel num_threads(ploidies.size()) + { + #pragma omp for + for (int tau : ploidies) + { + std::string dir_with_results_prefix = "ploidy_" + std::to_string(tau) + "_optim_results_"; + omp_set_lock(&lck); + Params::bayes_opt_bobase::set_dir_with_results_prefix(dir_with_results_prefix); + bayes_opt::BOptimizer, acquifun, + acquiopt, initfun, statsfun> + boptimizer; + omp_unset_lock(&lck); + boptimizer.optimize(eval_func(tau, sampleCopyNumber)); + + std::string filename = boptimizer.res_dir() + "/tau-" + std::to_string(tau) + "-alpha-" + std::to_string(boptimizer.best_sample()(0)); + std::ofstream(filename.c_str()); + + #pragma omp critical + best_score_alpha_per_tau.insert({tau, std::make_pair(boptimizer.best_observation()(0), boptimizer.best_sample()(0))}); + } + } + omp_destroy_lock(&lck); + } + float best_purity = -INFINITY; + float best_score = -INFINITY; + float best_tau = -1; + std::string clusteringOutputDir = outputDir+"/clustering_results"; + boost::filesystem::create_directories(clusteringOutputDir); +#pragma omp parallel num_threads(ploidies.size()) + { +#pragma omp for + for (int i = 0; i < best_score_alpha_per_tau.size(); i++) + { + auto x = best_score_alpha_per_tau.begin(); + std::advance(x, i); + double score_on_trunc = x->second.first; + double purity = x->second.second; + int tau = x->first; + + auto start = std::chrono::high_resolution_clock::now(); + double score_on_full = sampleCopyNumber.processGMM(clusteringOutputDir + "/res-" + std::to_string(tau) + "-" + std::to_string(purity), tau, purity, true, sampleCopyNumber.getDataSubsamplingRateInPloidyEvaluation(), true); + auto stop = std::chrono::high_resolution_clock::now(); + auto duration = std::chrono::duration_cast(stop - start); + + #pragma omp critical + { + std::cout << "processGMM (FULL) with tau/alpha:\t" << tau << " / " << purity << "\ttook " << duration.count() << " s" << std::endl; + std::cout << "TAU: " << tau << "\nBest sample: " << purity << " - Best observation (trunc): " << score_on_trunc << " - Best observation (full): " << score_on_full << std::endl; + if (score_on_full > best_score) + { + best_purity = purity; + best_score = score_on_full; + best_tau = tau; + } + } + } + } + + std::cout << "DIFF with TRUE purity:\t" << abs(truePurity - best_purity) << std::endl; + + best_result.insert({best_tau, std::make_pair(best_score, best_purity)}); + return best_result; +} diff --git a/src/bayes_opt.h b/src/bayes_opt.h new file mode 100644 index 0000000..cd707ca --- /dev/null +++ b/src/bayes_opt.h @@ -0,0 +1,35 @@ +#ifndef _BAYES_OPT_H +#define _BAYES_OPT_H + +#include +#include + +#include +#include "limbo/acqui/ei.hpp" +#include "limbo/opt/parallel_repeater.hpp" +#include "limbo/stat.hpp" + +#include "GenomeGMM.h" +#include "GenomeCopyNumber.h" + +struct Params; + + +double concrete_eval_func(double alpha, const Eigen::MatrixXd &data); + + +double my_eval_func(int tau, double alpha, const std::vector& ratio, + const std::vector& maf, GenomeGMM sampleGMM); + + +template +struct eval_func; + + +template +struct MeanFWModel; + + +std::map> findBestPurity(GenomeCopyNumber &sampleCopyNumber, std::vector ploidies, ConfigFile& cf, std::string outputDir); + +#endif \ No newline at end of file diff --git a/src/cumNormalDistr.cpp b/src/cumNormalDistr.cpp new file mode 100644 index 0000000..b829841 --- /dev/null +++ b/src/cumNormalDistr.cpp @@ -0,0 +1,65 @@ +// +// Created by gajaques on 6/1/22. +// + +#include "cumNormalDistr.h" +#include + +double calculateNormalCDF(double x, double mu, double sigma) +{ + // constants + double a1 = 0.254829592; + double a2 = -0.284496736; + double a3 = 1.421413741; + double a4 = -1.453152027; + double a5 = 1.061405429; + double p = 0.3275911; + + // Save the sign of x + int sign = 1; + if (x < mu) + sign = -1; + x = fabs(x-mu)/sqrt(2.0*sigma*sigma); + + // A&S formula 7.1.26 + double t = 1.0/(1.0 + p*x); + double y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-x*x); + + return 0.5*(1.0 + sign*y); +} + +void testNormalCDF() +{ + // Select a few input values + double x[] = + { + -3, + -1, + 0.0, + 0.5, + 2.1 + }; + + // Output computed by Mathematica + // y = Phi[x] + double y[] = + { + 0.00134989803163, + 0.158655253931, + 0.5, + 0.691462461274, + 0.982135579437 + }; + + int numTests = sizeof(x)/sizeof(double); + + double maxError = 0.0; + for (int i = 0; i < numTests; ++i) + { + double error = fabs(y[i] - calculateNormalCDF(x[i], 0, 2)); + if (error > maxError) + maxError = error; + } + + std::cout << "Maximum error: " << maxError << "\n"; +} \ No newline at end of file diff --git a/src/cumNormalDistr.h b/src/cumNormalDistr.h new file mode 100644 index 0000000..780c93a --- /dev/null +++ b/src/cumNormalDistr.h @@ -0,0 +1,14 @@ +// +// Created by John D. Cook. +// + +#ifndef SRC_CUMNORMALDISTR_H +#define SRC_CUMNORMALDISTR_H + +#include + +double calculateNormalCDF(double x, double mu, double sigma); +void testNormalCDF(); + + +#endif //SRC_CUMNORMALDISTR_H diff --git a/src/depend.mk b/src/depend.mk new file mode 100644 index 0000000..bd2bc9a --- /dev/null +++ b/src/depend.mk @@ -0,0 +1,8104 @@ +BAFpileup.o: BAFpileup.cpp /usr/include/stdc-predef.h BAFpileup.h \ + /usr/include/c++/9/string \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/bits/long-double.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \ + /usr/include/c++/9/bits/stringfwd.h /usr/include/c++/9/bits/memoryfwd.h \ + 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\ + /usr/include/x86_64-linux-gnu/bits/floatn-common.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/types/wint_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \ + /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \ + /usr/include/c++/9/bits/exception_ptr.h \ + /usr/include/c++/9/bits/exception_defines.h \ + /usr/include/c++/9/bits/cxxabi_init_exception.h \ + /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \ + /usr/include/c++/9/new /usr/include/c++/9/bits/nested_exception.h \ + /usr/include/c++/9/bits/move.h /usr/include/c++/9/bits/concept_check.h \ + /usr/include/c++/9/type_traits /usr/include/c++/9/bits/char_traits.h \ + /usr/include/c++/9/bits/stl_algobase.h \ + /usr/include/c++/9/bits/functexcept.h \ + /usr/include/c++/9/bits/cpp_type_traits.h \ + /usr/include/c++/9/ext/type_traits.h \ + /usr/include/c++/9/ext/numeric_traits.h \ + /usr/include/c++/9/bits/stl_pair.h \ + /usr/include/c++/9/bits/stl_iterator_base_types.h \ + /usr/include/c++/9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/9/debug/assertions.h \ + /usr/include/c++/9/bits/stl_iterator.h \ + /usr/include/c++/9/bits/ptr_traits.h /usr/include/c++/9/debug/debug.h \ + /usr/include/c++/9/bits/predefined_ops.h /usr/include/c++/9/cstdint \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h /usr/include/stdint.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/timesize.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/time64.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-intn.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-uintn.h \ + /usr/include/c++/9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \ + /usr/include/c++/9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endianness.h \ + /usr/include/c++/9/bits/ios_base.h /usr/include/c++/9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/time_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timespec.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h \ + /usr/include/x86_64-linux-gnu/bits/cpu-set.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timeval.h \ + /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/timer_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/thread-shared-types.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h \ + /usr/include/x86_64-linux-gnu/bits/struct_mutex.h \ + /usr/include/x86_64-linux-gnu/bits/struct_rwlock.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/bits/locale_classes.h /usr/include/c++/9/string \ + /usr/include/c++/9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \ + /usr/include/c++/9/ext/new_allocator.h \ + /usr/include/c++/9/bits/ostream_insert.h \ + /usr/include/c++/9/bits/cxxabi_forced.h \ + /usr/include/c++/9/bits/stl_function.h \ + /usr/include/c++/9/backward/binders.h \ + /usr/include/c++/9/bits/range_access.h \ + /usr/include/c++/9/initializer_list \ + /usr/include/c++/9/bits/basic_string.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/uintn-identity.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/types/sigset_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h \ + /usr/include/alloca.h /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/c++/9/bits/std_abs.h /usr/include/c++/9/cstdio \ + /usr/include/stdio.h /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc \ + /usr/include/c++/9/bits/locale_classes.tcc \ + /usr/include/c++/9/system_error \ + /usr/include/x86_64-linux-gnu/c++/9/bits/error_constants.h \ + /usr/include/c++/9/stdexcept /usr/include/c++/9/streambuf \ + /usr/include/c++/9/bits/streambuf.tcc \ + /usr/include/c++/9/bits/basic_ios.h \ + /usr/include/c++/9/bits/locale_facets.h /usr/include/c++/9/cwctype \ + /usr/include/wctype.h /usr/include/x86_64-linux-gnu/bits/wctype-wchar.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/ctype_base.h \ + /usr/include/c++/9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/ctype_inline.h \ + /usr/include/c++/9/bits/locale_facets.tcc \ + /usr/include/c++/9/bits/basic_ios.tcc \ + /usr/include/c++/9/bits/ostream.tcc /usr/include/c++/9/istream \ + /usr/include/c++/9/bits/istream.tcc /usr/include/c++/9/vector \ + /usr/include/c++/9/bits/stl_construct.h \ + /usr/include/c++/9/bits/stl_uninitialized.h \ + /usr/include/c++/9/bits/stl_vector.h \ + /usr/include/c++/9/bits/stl_bvector.h /usr/include/c++/9/bits/vector.tcc \ + myFunc.h /usr/include/c++/9/sstream /usr/include/c++/9/bits/sstream.tcc \ + /usr/include/c++/9/math.h /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ + /usr/include/x86_64-linux-gnu/bits/libm-simd-decl-stubs.h \ + /usr/include/x86_64-linux-gnu/bits/flt-eval-method.h \ + /usr/include/x86_64-linux-gnu/bits/fp-logb.h \ + /usr/include/x86_64-linux-gnu/bits/fp-fast.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-helper-functions.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-narrow.h \ + /usr/include/x86_64-linux-gnu/bits/iscanonical.h \ + /usr/include/c++/9/fstream /usr/include/c++/9/bits/codecvt.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++io.h \ + /usr/include/c++/9/bits/fstream.tcc /usr/include/c++/9/algorithm \ + /usr/include/c++/9/utility /usr/include/c++/9/bits/stl_relops.h \ + /usr/include/c++/9/bits/stl_algo.h \ + /usr/include/c++/9/bits/algorithmfwd.h \ + /usr/include/c++/9/bits/stl_heap.h /usr/include/c++/9/bits/stl_tempbuf.h \ + /usr/include/c++/9/bits/uniform_int_dist.h /usr/include/c++/9/limits \ + linreg.h ap.h /usr/include/c++/9/stdlib.h /usr/include/c++/9/list \ + /usr/include/c++/9/bits/stl_list.h \ + /usr/include/c++/9/bits/allocated_ptr.h \ + /usr/include/c++/9/ext/aligned_buffer.h /usr/include/c++/9/bits/list.tcc \ + apvt.h ialglib.h descriptivestatistics.h gammafunc.h normaldistr.h \ + igammaf.h hblas.h reflections.h creflections.h sblas.h ablasf.h ablas.h \ + ortfac.h blas.h rotations.h bdsvd.h svd.h /usr/include/string.h \ + /usr/include/strings.h /usr/include/c++/9/map \ + /usr/include/c++/9/bits/stl_tree.h /usr/include/c++/9/bits/stl_map.h \ + /usr/include/c++/9/tuple /usr/include/c++/9/array \ + /usr/include/c++/9/bits/uses_allocator.h \ + /usr/include/c++/9/bits/invoke.h /usr/include/c++/9/bits/stl_multimap.h \ + /usr/include/c++/9/bits/erase_if.h KernelVector.h +ConfigFile.o: ConfigFile.cpp /usr/include/stdc-predef.h ConfigFile.h \ + /usr/include/c++/9/string \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/bits/long-double.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \ + /usr/include/c++/9/bits/stringfwd.h /usr/include/c++/9/bits/memoryfwd.h \ + /usr/include/c++/9/bits/char_traits.h \ + /usr/include/c++/9/bits/stl_algobase.h \ + /usr/include/c++/9/bits/functexcept.h \ + /usr/include/c++/9/bits/exception_defines.h \ + /usr/include/c++/9/bits/cpp_type_traits.h \ + /usr/include/c++/9/ext/type_traits.h \ + /usr/include/c++/9/ext/numeric_traits.h \ + /usr/include/c++/9/bits/stl_pair.h /usr/include/c++/9/bits/move.h \ + /usr/include/c++/9/bits/concept_check.h /usr/include/c++/9/type_traits \ + /usr/include/c++/9/bits/stl_iterator_base_types.h \ + /usr/include/c++/9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/9/debug/assertions.h \ + /usr/include/c++/9/bits/stl_iterator.h \ + /usr/include/c++/9/bits/ptr_traits.h /usr/include/c++/9/debug/debug.h \ + /usr/include/c++/9/bits/predefined_ops.h \ + /usr/include/c++/9/bits/postypes.h /usr/include/c++/9/cwchar \ + /usr/include/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/libc-header-start.h \ + /usr/include/x86_64-linux-gnu/bits/floatn.h \ + /usr/include/x86_64-linux-gnu/bits/floatn-common.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/types/wint_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \ + /usr/include/c++/9/cstdint \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h /usr/include/stdint.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/timesize.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/time64.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-intn.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-uintn.h \ + /usr/include/c++/9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \ + /usr/include/c++/9/ext/new_allocator.h /usr/include/c++/9/new \ + /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \ + /usr/include/c++/9/bits/exception_ptr.h \ + /usr/include/c++/9/bits/cxxabi_init_exception.h \ + /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \ + /usr/include/c++/9/bits/nested_exception.h \ + /usr/include/c++/9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \ + /usr/include/c++/9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/9/iosfwd \ + /usr/include/c++/9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endianness.h \ + /usr/include/c++/9/bits/ostream_insert.h \ + /usr/include/c++/9/bits/cxxabi_forced.h \ + /usr/include/c++/9/bits/stl_function.h \ + /usr/include/c++/9/backward/binders.h \ + /usr/include/c++/9/bits/range_access.h \ + /usr/include/c++/9/initializer_list \ + /usr/include/c++/9/bits/basic_string.h \ + /usr/include/c++/9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/time_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timespec.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h \ + /usr/include/x86_64-linux-gnu/bits/cpu-set.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timeval.h \ + /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/timer_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/thread-shared-types.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h \ + /usr/include/x86_64-linux-gnu/bits/struct_mutex.h \ + /usr/include/x86_64-linux-gnu/bits/struct_rwlock.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/uintn-identity.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/types/sigset_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h \ + /usr/include/alloca.h /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/c++/9/bits/std_abs.h /usr/include/c++/9/cstdio \ + /usr/include/stdio.h 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+ /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdio \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc /usr/include/c++/9/math.h \ + /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ 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/usr/include/c++/9/cwchar \ + /usr/include/wchar.h /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/types/wint_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h \ + /usr/include/c++/9/cstdint \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h /usr/include/stdint.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-uintn.h \ + /usr/include/c++/9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \ + /usr/include/c++/9/ext/new_allocator.h /usr/include/c++/9/new \ + /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \ + /usr/include/c++/9/bits/exception_ptr.h \ + /usr/include/c++/9/bits/cxxabi_init_exception.h \ + /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \ + /usr/include/c++/9/bits/nested_exception.h \ + /usr/include/c++/9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \ + /usr/include/c++/9/clocale /usr/include/locale.h \ + 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+ /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdio \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc /usr/include/c++/9/math.h \ + /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ 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\ + /usr/include/c++/9/debug/assertions.h \ + /usr/include/c++/9/bits/stl_iterator.h \ + /usr/include/c++/9/bits/ptr_traits.h /usr/include/c++/9/debug/debug.h \ + /usr/include/c++/9/bits/predefined_ops.h \ + /usr/include/c++/9/bits/postypes.h /usr/include/c++/9/cwchar \ + /usr/include/wchar.h /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/types/wint_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h \ + /usr/include/c++/9/cstdint \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h /usr/include/stdint.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-uintn.h \ + /usr/include/c++/9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \ + /usr/include/c++/9/ext/new_allocator.h /usr/include/c++/9/new \ + /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \ + /usr/include/c++/9/bits/exception_ptr.h \ + /usr/include/c++/9/bits/cxxabi_init_exception.h \ + /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \ + /usr/include/c++/9/bits/nested_exception.h \ + /usr/include/c++/9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \ + /usr/include/c++/9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/9/iosfwd \ + /usr/include/c++/9/cctype /usr/include/ctype.h \ + /usr/include/c++/9/bits/ostream_insert.h \ + /usr/include/c++/9/bits/cxxabi_forced.h \ + /usr/include/c++/9/bits/stl_function.h \ + /usr/include/c++/9/backward/binders.h \ + /usr/include/c++/9/bits/range_access.h \ + /usr/include/c++/9/initializer_list \ + /usr/include/c++/9/bits/basic_string.h \ + /usr/include/c++/9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h \ + /usr/include/x86_64-linux-gnu/bits/cpu-set.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdio \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc /usr/include/c++/9/math.h \ + /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ + /usr/include/x86_64-linux-gnu/bits/libm-simd-decl-stubs.h \ + /usr/include/x86_64-linux-gnu/bits/flt-eval-method.h \ + /usr/include/x86_64-linux-gnu/bits/fp-logb.h \ + /usr/include/x86_64-linux-gnu/bits/fp-fast.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-helper-functions.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-narrow.h \ + /usr/include/x86_64-linux-gnu/bits/iscanonical.h /usr/include/c++/9/list \ + /usr/include/c++/9/bits/stl_list.h \ + /usr/include/c++/9/bits/allocated_ptr.h \ + /usr/include/c++/9/ext/aligned_buffer.h /usr/include/c++/9/bits/list.tcc \ + /usr/include/c++/9/vector /usr/include/c++/9/bits/stl_construct.h \ + /usr/include/c++/9/bits/stl_uninitialized.h \ + /usr/include/c++/9/bits/stl_vector.h \ + /usr/include/c++/9/bits/stl_bvector.h /usr/include/c++/9/bits/vector.tcc \ + apvt.h ialglib.h gammafunc.h normaldistr.h igammaf.h +reflections.o: reflections.cpp /usr/include/stdc-predef.h reflections.h \ + ap.h /usr/include/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/libc-header-start.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/bits/long-double.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/timesize.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/time64.h \ + /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/c++/9/stdlib.h /usr/include/c++/9/cstdlib \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/os_defines.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/bits/floatn.h \ + /usr/include/x86_64-linux-gnu/bits/floatn-common.h \ + /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/time_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/timer_t.h \ + /usr/include/x86_64-linux-gnu/bits/stdint-intn.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endianness.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/uintn-identity.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/types/sigset_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timeval.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_timespec.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/thread-shared-types.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h \ + /usr/include/x86_64-linux-gnu/bits/struct_mutex.h \ + /usr/include/x86_64-linux-gnu/bits/struct_rwlock.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/c++/9/bits/std_abs.h /usr/include/c++/9/string \ + /usr/include/c++/9/bits/stringfwd.h /usr/include/c++/9/bits/memoryfwd.h \ + /usr/include/c++/9/bits/char_traits.h \ + /usr/include/c++/9/bits/stl_algobase.h \ + /usr/include/c++/9/bits/functexcept.h \ + /usr/include/c++/9/bits/exception_defines.h \ + /usr/include/c++/9/bits/cpp_type_traits.h \ + /usr/include/c++/9/ext/type_traits.h \ + /usr/include/c++/9/ext/numeric_traits.h \ + /usr/include/c++/9/bits/stl_pair.h /usr/include/c++/9/bits/move.h \ + /usr/include/c++/9/bits/concept_check.h /usr/include/c++/9/type_traits \ + /usr/include/c++/9/bits/stl_iterator_base_types.h \ + /usr/include/c++/9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/9/debug/assertions.h \ + /usr/include/c++/9/bits/stl_iterator.h \ + 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+ /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdio \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc /usr/include/c++/9/math.h \ + /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ + /usr/include/x86_64-linux-gnu/bits/libm-simd-decl-stubs.h \ + /usr/include/x86_64-linux-gnu/bits/flt-eval-method.h \ + /usr/include/x86_64-linux-gnu/bits/fp-logb.h \ + /usr/include/x86_64-linux-gnu/bits/fp-fast.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-helper-functions.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-narrow.h \ + /usr/include/x86_64-linux-gnu/bits/iscanonical.h /usr/include/c++/9/list \ + /usr/include/c++/9/bits/stl_list.h \ + /usr/include/c++/9/bits/allocated_ptr.h \ + /usr/include/c++/9/ext/aligned_buffer.h /usr/include/c++/9/bits/list.tcc \ + /usr/include/c++/9/vector /usr/include/c++/9/bits/stl_construct.h \ + /usr/include/c++/9/bits/stl_uninitialized.h \ + /usr/include/c++/9/bits/stl_vector.h \ + /usr/include/c++/9/bits/stl_bvector.h /usr/include/c++/9/bits/vector.tcc \ + apvt.h ialglib.h +rotations.o: rotations.cpp /usr/include/stdc-predef.h rotations.h ap.h \ + /usr/include/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/libc-header-start.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/bits/long-double.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h \ + /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/timesize.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/time64.h \ + /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h \ + /usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/c++/9/stdlib.h /usr/include/c++/9/cstdlib \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/os_defines.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/bits/floatn.h \ + /usr/include/x86_64-linux-gnu/bits/floatn-common.h \ + /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \ + /usr/include/x86_64-linux-gnu/bits/types/time_t.h \ + 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/usr/include/c++/9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \ + /usr/include/c++/9/ext/new_allocator.h /usr/include/c++/9/new \ + /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \ + /usr/include/c++/9/bits/exception_ptr.h \ + /usr/include/c++/9/bits/cxxabi_init_exception.h \ + /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \ + /usr/include/c++/9/bits/nested_exception.h \ + /usr/include/c++/9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \ + /usr/include/c++/9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/9/iosfwd \ + /usr/include/c++/9/cctype /usr/include/ctype.h \ + /usr/include/c++/9/bits/ostream_insert.h \ + /usr/include/c++/9/bits/cxxabi_forced.h \ + /usr/include/c++/9/bits/stl_function.h \ + /usr/include/c++/9/backward/binders.h \ + /usr/include/c++/9/bits/range_access.h \ + /usr/include/c++/9/initializer_list \ + /usr/include/c++/9/bits/basic_string.h \ + /usr/include/c++/9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h \ + /usr/include/x86_64-linux-gnu/bits/cpu-set.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \ + /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \ + /usr/include/c++/9/ext/alloc_traits.h \ + /usr/include/c++/9/bits/alloc_traits.h \ + /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdio \ + /usr/include/c++/9/cerrno /usr/include/errno.h \ + /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/x86_64-linux-gnu/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + /usr/include/x86_64-linux-gnu/bits/types/error_t.h \ + /usr/include/c++/9/bits/functional_hash.h \ + /usr/include/c++/9/bits/basic_string.tcc /usr/include/c++/9/math.h \ + /usr/include/c++/9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/math-vector.h \ + /usr/include/x86_64-linux-gnu/bits/libm-simd-decl-stubs.h \ + /usr/include/x86_64-linux-gnu/bits/flt-eval-method.h \ + /usr/include/x86_64-linux-gnu/bits/fp-logb.h \ + /usr/include/x86_64-linux-gnu/bits/fp-fast.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-helper-functions.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls-narrow.h \ + /usr/include/x86_64-linux-gnu/bits/iscanonical.h /usr/include/c++/9/list \ + /usr/include/c++/9/bits/stl_list.h \ + /usr/include/c++/9/bits/allocated_ptr.h \ + /usr/include/c++/9/ext/aligned_buffer.h /usr/include/c++/9/bits/list.tcc \ + /usr/include/c++/9/vector /usr/include/c++/9/bits/stl_construct.h \ + /usr/include/c++/9/bits/stl_uninitialized.h \ + /usr/include/c++/9/bits/stl_vector.h \ + /usr/include/c++/9/bits/stl_bvector.h /usr/include/c++/9/bits/vector.tcc \ + apvt.h ialglib.h hblas.h reflections.h creflections.h sblas.h ablasf.h \ + ablas.h ortfac.h blas.h rotations.h bdsvd.h diff --git a/src/gaussianKernel.cpp b/src/gaussianKernel.cpp new file mode 100644 index 0000000..6429baf --- /dev/null +++ b/src/gaussianKernel.cpp @@ -0,0 +1,68 @@ +// +// Created by gajaques on 6/1/22. +// + +#include "gaussianKernel.h" +#include +#include + +gaussianKernel::gaussianKernel() {} +gaussianKernel::~gaussianKernel() {} + +std::vector computeGaussianKernel(const std::vector& x, float x_value, float cov) +{ + int n = x.size(); + std::vector kernel(n); + float sum_kernel = 0; + for (int i = 0; i < n; i++) { + kernel[i] = exp(-pow(x[i] - x_value, 2)/(2*pow(cov,2))); + sum_kernel += kernel[i]; + } + for (int i = 0; i < n; i++) { + kernel[i] = kernel[i]/sum_kernel; + } + return kernel; +} + +float applyGaussianKernelToValues(const std::vector& kernel, const std::vector& interval_x_values) +{ + if (kernel.size() != interval_x_values.size()) { + std::cerr << "Error: the kernel needs to have the same size as the vector passed by argument" << std::endl; + } + float x_filtered = 0; + for (unsigned int i = 0; i < interval_x_values.size(); i++) { + x_filtered += kernel[i] * interval_x_values[i]; + } + return x_filtered; +} + +std::vector applyGaussianKernel(const std::vector& x, float cov, int size) +{ + int n = x.size(); + // Round size to the nearest odd + int kernel_width = 1; + if (floor(size*cov) != 0) { + kernel_width = floor(size * cov); + } else { + kernel_width = ceil(size * cov); + } + + int hkernel_width = floor(kernel_width/2); + std::vector interval(kernel_width); + std::vector kernel(kernel_width); + std::vector x_filtered(n); + for (int i = 0; i < n; i++) { + if ((i >= hkernel_width) & ((n-i) > hkernel_width)) { + interval = {x.begin() + i - 2, x.begin() + i + 2}; + } else if ((i < hkernel_width) & ((n-i) > hkernel_width)) { + interval = {x.begin(), x.begin() + i + 2}; + } else if ((i >= hkernel_width) & ((n-i) <= hkernel_width)) { + interval = {x.begin() + i - 2, x.end()}; + } else { + interval = x; + } + kernel = computeGaussianKernel(interval, x[i], cov); + x_filtered[i] = applyGaussianKernelToValues(kernel, interval); + } + return x_filtered; +} \ No newline at end of file diff --git a/src/gaussianKernel.h b/src/gaussianKernel.h new file mode 100644 index 0000000..b3ec2ee --- /dev/null +++ b/src/gaussianKernel.h @@ -0,0 +1,23 @@ +// +// Created by gajaques on 6/1/22. +// + +#ifndef SRC_GAUSSIANKERNEL_H +#define SRC_GAUSSIANKERNEL_H + +#include + +class gaussianKernel +{ +public: + gaussianKernel(); + ~gaussianKernel(); +}; + +std::vector computeGaussianKernel(const std::vector& x, float x_value, float cov); +float applyGaussianKernelToValues(const std::vector& kernel, const std::vector& interval_x_values); +std::vector applyGaussianKernel(const std::vector& x, float cov, int size = 4); + + + +#endif //SRC_GAUSSIANKERNEL_H diff --git a/src/main.cpp b/src/main.cpp index e5f615e..73f54af 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -28,9 +28,11 @@ A copy of the GNU General Public License is available at #include "SeekSubclones.h" #include "version.h" +#include #include +#include #include - +#include using namespace std ; @@ -170,7 +172,10 @@ int main(int argc, char *argv[]) print_version(); - const char* conf_file = get_conf_file(argc, argv); + //const char* conf_file = "/home/gajaques/Documents/project/config_file_fast.txt"; +// const char* conf_file = "/home/gajaques/Documents/project/ploidy-purity-cpp/configs/snps-tau5-alpha60.txt"; + const char* conf_file = get_conf_file(argc, argv); + ConfigFile cf(conf_file); @@ -306,6 +311,18 @@ int main(int argc, char *argv[]) } string outputDir = (std::string)cf.Value("general","outputDir","."); + + auto t = std::time(nullptr); + auto tm = *std::localtime(&t); + + std::ostringstream oss; + oss << std::put_time(&tm, "%d-%m-%Y-%H-%M-%S"); + outputDir = outputDir + '-' + oss.str(); + boost::filesystem::create_directories(outputDir); + std::cout << "Created output DIR: " << outputDir << std::endl; + string logFile = outputDir + "/runtime_logs.txt"; + string logFileErr = outputDir + "/stderr_logs.txt"; + if ( access( outputDir.c_str(), 0 ) == 0 ) { struct stat status; stat( outputDir.c_str(), &status ); @@ -322,6 +339,16 @@ int main(int argc, char *argv[]) exit(-1); } + boost::filesystem::copy_file(conf_file, outputDir+"/"+"freec_config.txt"); + std::cout << "Configuration is saved to:\t" << outputDir+"/"+"freec_config.txt" << std::endl; + + std::cout << logFileErr << " - subsequent stderr is redirected here" << std::endl; + freopen(logFileErr.c_str(),"w",stderr); + + std::cout << logFile << " - subsequent stdout is redirected here" << std::endl; + freopen(logFile.c_str(),"w",stdout); + + bool has_dirWithFastaSeq = cf.hasValue("general","chrFiles"); string dirWithFastaSeq = (std::string)cf.Value("general","chrFiles",""); if (has_dirWithFastaSeq) { @@ -794,6 +821,10 @@ int main(int argc, char *argv[]) makingPileup = true; } + int dataSubsamplingRateInPuritySearch = (int)cf.Value("bayesopt","dataSubsamplingRateInPuritySearch",1000); + int dataSubsamplingRateInPloidyEvaluation = (int)cf.Value("bayesopt","dataSubsamplingRateInPloidyEvaluation",50); + bool doRescaleRatio = (std::string)cf.Value("bayesopt","doRescaleRatio","true") == "true" ? true : false; + GenomeCopyNumber sampleCopyNumber; sampleCopyNumber.setSamtools(pathToSamtools, SambambaThreads); sampleCopyNumber.setSambamba(pathToSambamba, SambambaThreads); @@ -802,6 +833,9 @@ int main(int argc, char *argv[]) sampleCopyNumber.setmakingPileup(makingPileup); sampleCopyNumber.setIfLogged(logLogNorm); + sampleCopyNumber.setDataSubsamplingRateInPuritySearch(dataSubsamplingRateInPuritySearch); + sampleCopyNumber.setDataSubsamplingRateInPloidyEvaluation(dataSubsamplingRateInPloidyEvaluation); + sampleCopyNumber.setDoRescaleRatio(doRescaleRatio); GenomeCopyNumber controlCopyNumber; controlCopyNumber.setSamtools(pathToSamtools, SambambaThreads); @@ -1110,31 +1144,31 @@ int main(int argc, char *argv[]) } - int bestPloidy= ploidies[min_element(RSS.begin(),RSS.end())-RSS.begin()]; - cout << "..Best ploidy set to "<> bestResult = findBestPurity(sampleCopyNumber, ploidies, cf, outputDir); + int bestTau = bestResult.begin()->first; + double bestPurity = bestResult.begin()->second.second; + double bestScore = bestResult.begin()->second.first; + auto stop = std::chrono::high_resolution_clock::now(); + auto duration = std::chrono::duration_cast(stop - start); + if (ploidies.size() == 1){ + cout << "findBestPurity with tau:\t" << bestTau << "\ttook " << duration.count() << " s" << endl; + } else { + cout << "findBestPurity for set of ploidies of size:\t" << ploidies.size() << "\ttook " << duration.count() << " s" << endl; + } + std::cout << "Best score: " << bestScore << "\nBEST purity/ploidy: " << bestPurity << "/" << bestTau << endl; + + // END //printing parameters and summary into the Information file easy to parse std::ofstream file ((myName+"_info.txt").c_str()); diff --git a/src/myFunc.cpp b/src/myFunc.cpp index 02893b2..67fa99a 100644 --- a/src/myFunc.cpp +++ b/src/myFunc.cpp @@ -22,6 +22,7 @@ A copy of the GNU General Public License is available at #include "myFunc.h" #include #include +#include "gaussianKernel.h" #if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__)) //x32 Windows definitions @@ -308,6 +309,7 @@ void readFileWithGenomeInfo(const std::string &chrLenFileName, std::vector0) { names.push_back(name); lengths.push_back(value); - //cout << name << "\t" << value << "\n"; + cout << name << "\t" << value << "\n"; } } @@ -2741,3 +2743,106 @@ char* getLine(char* buffer, int buffer_size, FILE* stream, std::string& line) return quartiles; } +// Added by Gara +// Function to find first index >= x in a sorted vector +int lowerIndex(const std::vector& sorted_vector, int n, float x) +{ + int l = 0, h = n - 1; + while (l <= h) { + int mid = (l + h) / 2; + if (sorted_vector[mid] >= x) { + h = mid - 1; + } + else { + l = mid + 1; + } + } + return l; +} + +// Function to find last index <= y in a sorted vector +int upperIndex(const std::vector& sorted_vector, int n, float y) +{ + int l = 0, h = n - 1; + while (l <= h) { + int mid = (l + h) / 2; + if (sorted_vector[mid] <= y) { + l = mid + 1; + } + else { + h = mid - 1; + } + } + return h; +} + +// Function to count elements within given range x-y in a sorted vector +int countInRange(const std::vector& sorted_vector, int n, float x, float y) +{ + // initialize result + int count = 0; + count = upperIndex(sorted_vector, n, y) - lowerIndex(sorted_vector, n, x) + 1; + return count; +} + +// Function that counts how many elements of a vector fall in each bin of bins +std::vector makeHistogramOfCounts(const std::vector& vec, const std::vector& bins) +{ + int n = bins.size(); + std::cout << "int n = bins.size();" << std::endl; + std::vector counts(n-1); + std::vector sorted_vector = vec; + std::sort(sorted_vector.begin(), sorted_vector.end()); + for (int i = 0; i < (n-1); i++) { + /*std::cout << "Sorted vector: "; + for (int j = 0; j < 10; j++) { + std::cout << sorted_vector[j] << " "; + } + std::cout << std::endl; + std::cout << "x value: " << bins[i] << std::endl; + std::cout << "y value: " << bins[i+1] << std::endl;*/ + float c = countInRange(sorted_vector, sorted_vector.size(), bins[i], bins[i+1]); + counts[i] = c; + } + return counts; +} + +std::vector gaussianFilter1d(const std::vector& vec, float cov, int size) +{ + return applyGaussianKernel(vec, cov, size); +} + +std::map findPeaks(const std::vector& counts, float cov, float min_height, int min_distance) +{ + int n = counts.size(); + std::vector filtered_counts(n); + filtered_counts = gaussianFilter1d(counts, cov, 4); + + std::map peaks; + float max_count = 0; + for (int i = 0; i < n; i++) { + if (filtered_counts[i] > max_count) { + max_count = filtered_counts[i]; + if (filtered_counts[i+1] < max_count) { + if (max_count >= min_height) { + if (peaks.empty()) { + peaks[i] = max_count; + } else { + std::map::iterator it; + it = --peaks.end(); + int distance = i - it->first; + float count = it->second; + if (distance >= min_distance) { + peaks[i] = max_count; + } else if (max_count > count) { + peaks.erase(it->first); + peaks[i] = max_count; + } + } + } + } + } + } + return peaks; +} + diff --git a/src/myFunc.h b/src/myFunc.h index f9826c9..f25c260 100644 --- a/src/myFunc.h +++ b/src/myFunc.h @@ -16,6 +16,7 @@ #include "linreg.h" #include "normaldistr.h" #include +#include #ifndef NA #define NA -1 @@ -32,7 +33,7 @@ #define HOMOZYG_MEAN 0.11 #define middleComponentMinWeight 0.1 - #define pi 3.14159 + #define PI_ 3.14159 #define ZERO 0.0000000001 #define MAX_BUFFER 2048 @@ -153,6 +154,17 @@ std::vector get_quartiles(std::vector vect); int calculateTotalLength(std::vector lefts,std::vector rights); bool checkChrLen(const std::string &chrLenFile,const std::string &targetBed) ; +// Added by Gara +// Functions useful for making the histogram +int lowerIndex(const std::vector& sorted_vector, int n, float x); +int upperIndex(const std::vector& sorted_vector, int n, float y); +int countInRange(const std::vector& sorted_vector, int n, float x, float y); +std::vector makeHistogramOfCounts(const std::vector& vec, const std::vector& bins); +std::vector gaussianFilter1d(const std::vector& vec, float cov, int size = 4); +std::map findPeaks(const std::vector& freqs, float cov, float min_height, int min_distance); + + + #ifdef _WIN32 double expm1(double x); double log1p(double x); From 54abebd6da973e80701a2fab9f7ffeadb535a075 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Thu, 1 Sep 2022 14:48:45 +0200 Subject: [PATCH 2/7] chore: upd version.h --- src/version.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/version.h b/src/version.h index 727c5c1..402cf29 100644 --- a/src/version.h +++ b/src/version.h @@ -2,8 +2,8 @@ #ifndef VERSION_H #define VERSION_H -const double VERSION_OFFSET = 3; -const double FREEC_VERSION = 11.6; +const double VERSION_OFFSET = 0; +const double FREEC_VERSION = 12.0; const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET; #endif From 103b36d0d115e7e0f9905383b00a49f9d03656d0 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Fri, 2 Sep 2022 01:16:35 +0200 Subject: [PATCH 3/7] refactor: remove debug code from bayes_opt --- src/bayes_opt.cpp | 84 +++++++++++------------------------------------ 1 file changed, 20 insertions(+), 64 deletions(-) diff --git a/src/bayes_opt.cpp b/src/bayes_opt.cpp index 9752216..170a3ff 100644 --- a/src/bayes_opt.cpp +++ b/src/bayes_opt.cpp @@ -122,11 +122,8 @@ void misc_eval(GenomeCopyNumber genomeCopyNumber, int tau, double alpha) std::map> findBestPurity(GenomeCopyNumber &sampleCopyNumber, std::vector ploidies, ConfigFile &cf, std::string outputDir) { - // TMP int optimObjectiveCalls = (int)cf.Value("bayesopt", "optimObjectiveCalls", 1); double kernelNoise = (double)cf.Value("bayesopt", "kernelNoise", 1e-10); - double truePurity = (double)cf.Value("bayesopt", "truePurity", 0.5); - bool runTruePurity = (bool)cf.Value("bayesopt", "runTruePurity", false); Params::stop_maxiterations::set_iterations(optimObjectiveCalls); Params::kernel::set_noise(kernelNoise); Params::bayes_opt_bobase::set_base_dir(outputDir); @@ -152,73 +149,32 @@ std::map> findBestPurity(GenomeCopyNumber &sample std::map> best_score_alpha_per_tau; std::map> best_result; - if (runTruePurity == true && truePurity != 0.5) - { - int truePloidy = (int)cf.Value("bayesopt", "truePloidy", 0); - if (truePloidy == 0) {std::cout << "truePloidy not provided. Skipping evaluation for the correct pair" << std::endl;} - else { - std::cout << "/* misc_eval(sampleCopyNumber, truePloidy, truePurity); */" << std::endl; - std::cout << "/* misc_eval(sampleCopyNumber, " << truePloidy << ", " << truePurity << "); */" << std::endl; - misc_eval(sampleCopyNumber, truePloidy, truePurity); - } - } - else if (runTruePurity == true) - { - std::cout << "/* runTruePurity == true BUT truePurity is NOT supplied */" << std::endl; - } + omp_lock_t lck; + omp_init_lock(&lck); - std::vector queryPurities; - std::vector strs; - std::string queryPurities_str = (std::string)cf.Value("bayesopt", "queryPurities", ""); - split(queryPurities_str, ',', strs); - if (strs.size() > 1) +#pragma omp parallel num_threads(ploidies.size()) { - std::cout << "QUERY sample purities"; - for (unsigned int i = 0; i < strs.size(); i++) +#pragma omp for + for (int tau : ploidies) { - queryPurities.push_back(std::stod(strs[i].c_str())); - std::cout << "/* misc_eval(sampleCopyNumber, " << ploidies.at(0) << ", " << queryPurities.back() << "); */" << std::endl; - misc_eval(sampleCopyNumber, ploidies.at(0), queryPurities.back()); - } - exit(0); - } - else - { - std::cout << "Skipping QUERY sample purities: " << queryPurities_str << std::endl; - } - - bool queryPloidies = (bool)cf.Value("bayesopt", "queryPloidies", false); - if (queryPloidies){ - for (int tau : ploidies){ - best_score_alpha_per_tau.insert({tau, std::make_pair(1, truePurity)}); - } - } else { - omp_lock_t lck; - omp_init_lock(&lck); + std::string dir_with_results_prefix = "ploidy_" + std::to_string(tau) + "_optim_results_"; + omp_set_lock(&lck); + Params::bayes_opt_bobase::set_dir_with_results_prefix(dir_with_results_prefix); + bayes_opt::BOptimizer, acquifun, + acquiopt, initfun, statsfun> + boptimizer; + omp_unset_lock(&lck); + boptimizer.optimize(eval_func(tau, sampleCopyNumber)); + + std::string filename = boptimizer.res_dir() + "/tau-" + std::to_string(tau) + "-alpha-" + std::to_string(boptimizer.best_sample()(0)); + std::ofstream(filename.c_str()); - #pragma omp parallel num_threads(ploidies.size()) - { - #pragma omp for - for (int tau : ploidies) - { - std::string dir_with_results_prefix = "ploidy_" + std::to_string(tau) + "_optim_results_"; - omp_set_lock(&lck); - Params::bayes_opt_bobase::set_dir_with_results_prefix(dir_with_results_prefix); - bayes_opt::BOptimizer, acquifun, - acquiopt, initfun, statsfun> - boptimizer; - omp_unset_lock(&lck); - boptimizer.optimize(eval_func(tau, sampleCopyNumber)); - - std::string filename = boptimizer.res_dir() + "/tau-" + std::to_string(tau) + "-alpha-" + std::to_string(boptimizer.best_sample()(0)); - std::ofstream(filename.c_str()); - - #pragma omp critical - best_score_alpha_per_tau.insert({tau, std::make_pair(boptimizer.best_observation()(0), boptimizer.best_sample()(0))}); - } +#pragma omp critical + best_score_alpha_per_tau.insert({tau, std::make_pair(boptimizer.best_observation()(0), boptimizer.best_sample()(0))}); } - omp_destroy_lock(&lck); } + omp_destroy_lock(&lck); + float best_purity = -INFINITY; float best_score = -INFINITY; float best_tau = -1; From 3c520d76a1eb4eb7b61d904ddc273079884cf9f0 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Fri, 2 Sep 2022 01:24:46 +0200 Subject: [PATCH 4/7] refactor: remove some comments, minor extras --- src/GenomeCopyNumber.cpp | 11 +++-------- src/bayes_opt.cpp | 4 ++-- src/bayes_opt.h | 2 +- 3 files changed, 6 insertions(+), 11 deletions(-) diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp index 00695db..aa7b1c7 100644 --- a/src/GenomeCopyNumber.cpp +++ b/src/GenomeCopyNumber.cpp @@ -4600,13 +4600,8 @@ bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty GenomeGMM sampleGMM; - auto start = std::chrono::high_resolution_clock::now(); fixExpectedRatioAndMAF(sampleGMM, genome_ratio_full, genome_maf_smoothed_full, tau, alpha); sampleGMM.printExpectedRatioAndMAF(outFile, tau, alpha); - auto stop = std::chrono::high_resolution_clock::now(); - auto duration = std::chrono::duration_cast(stop - start); -#pragma omp critical - cout << "fixExpectedRatioAndMAF with tau/alpha:\t" << tau << " / " << alpha << "\ttook " << duration.count() << " s" << endl; std::vector genome_ratio_smoothed; std::vector genome_maf_smoothed; @@ -4628,10 +4623,10 @@ bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty std::cout << "take_subsample_flag:\t" << take_subsample_flag << std::endl; std::cout << "Size of genome_maf_smoothed for fitting:\t" << genome_maf_smoothed.size() << "\t\% of full:\t" << (float)genome_maf_smoothed.size() / genome_maf_smoothed_full.size()<< std::endl; - start = std::chrono::high_resolution_clock::now(); + auto start = std::chrono::high_resolution_clock::now(); double bestL = sampleGMM.fitPredict(tau, alpha, genome_ratio_smoothed, genome_maf_smoothed); - stop = std::chrono::high_resolution_clock::now(); - duration = std::chrono::duration_cast(stop - start); + auto stop = std::chrono::high_resolution_clock::now(); + auto duration = std::chrono::duration_cast(stop - start); #pragma omp critical cout << "fitPredict with tau/alpha:\t" << tau << " / " << alpha << "\ttook " << duration.count() << " s" << endl; diff --git a/src/bayes_opt.cpp b/src/bayes_opt.cpp index 170a3ff..98b6b97 100644 --- a/src/bayes_opt.cpp +++ b/src/bayes_opt.cpp @@ -58,7 +58,7 @@ struct Params }; }; -double my_eval_func(int tau, double alpha, GenomeCopyNumber genomeCopyNumber) +double optim_scoring_func(int tau, double alpha, GenomeCopyNumber genomeCopyNumber) { auto start = std::chrono::high_resolution_clock::now(); double score = genomeCopyNumber.processGMM("/tmp/res-" + std::to_string(tau) + "-" + std::to_string(alpha), tau, alpha, true, genomeCopyNumber.getDataSubsamplingRateInPuritySearch(), false); @@ -99,7 +99,7 @@ struct eval_func Eigen::VectorXd operator()(const Eigen::VectorXd &x) const { double alpha = x(0); - double score = my_eval_func(tau, alpha, genomeCopyNumber); + double score = optim_scoring_func(tau, alpha, genomeCopyNumber); return tools::make_vector(score); } }; diff --git a/src/bayes_opt.h b/src/bayes_opt.h index cd707ca..77a1eb6 100644 --- a/src/bayes_opt.h +++ b/src/bayes_opt.h @@ -18,7 +18,7 @@ struct Params; double concrete_eval_func(double alpha, const Eigen::MatrixXd &data); -double my_eval_func(int tau, double alpha, const std::vector& ratio, +double optim_scoring_func(int tau, double alpha, const std::vector& ratio, const std::vector& maf, GenomeGMM sampleGMM); From f3d77b12ba8db3adc5d427bd474f5fa0355b0138 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Sat, 3 Sep 2022 00:09:29 +0200 Subject: [PATCH 5/7] refactor: tweak GMM fitting defaults, set maxIter dynamically --- .gitmodules | 3 +++ limbo | 1 + src/GenomeCopyNumber.cpp | 17 ++++++++++++++--- src/GenomeCopyNumber.h | 5 +++++ src/GenomeGMM.cpp | 11 ++--------- src/GenomeGMM.h | 2 +- src/bayes_opt.cpp | 4 +--- src/main.cpp | 6 ++++-- 8 files changed, 31 insertions(+), 18 deletions(-) create mode 100644 .gitmodules create mode 160000 limbo diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..fcd6e03 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "limbo"] + path = limbo + url = https://github.com/kirilllzaitsev/limbo.git diff --git a/limbo b/limbo new file mode 160000 index 0000000..9c8ab62 --- /dev/null +++ b/limbo @@ -0,0 +1 @@ +Subproject commit 9c8ab62645514077c6bfdc505b32b7c6a2505681 diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp index aa7b1c7..4835615 100644 --- a/src/GenomeCopyNumber.cpp +++ b/src/GenomeCopyNumber.cpp @@ -35,9 +35,10 @@ GenomeCopyNumber::GenomeCopyNumber(void) isMappUsed_=false; totalNumberOfPairs_=0; normalNumberOfPairs_=0; - dataSubsamplingRateInPuritySearch = 1000; - dataSubsamplingRateInPloidyEvaluation = 50; + dataSubsamplingRateInPuritySearch = 700; + dataSubsamplingRateInPloidyEvaluation = 2; doRescaleRatio=true; + maxIterGMM=8; } bool GenomeCopyNumber::isMappUsed() {return isMappUsed_;} @@ -4368,6 +4369,11 @@ void GenomeCopyNumber::setDataSubsamplingRateInPloidyEvaluation(int _dataSubsamp dataSubsamplingRateInPloidyEvaluation = _dataSubsamplingRateInPloidyEvaluation; } +void GenomeCopyNumber::setMaxIterGMM(int _maxIterGMM) +{ + maxIterGMM = _maxIterGMM; +} + int GenomeCopyNumber::getDataSubsamplingRateInPuritySearch() { return dataSubsamplingRateInPuritySearch; @@ -4378,6 +4384,11 @@ int GenomeCopyNumber::getDataSubsamplingRateInPloidyEvaluation() return dataSubsamplingRateInPloidyEvaluation; } +int GenomeCopyNumber::getMaxIterGMM() +{ + return maxIterGMM; +} + void GenomeCopyNumber::setDoRescaleRatio(bool _doRescaleRatio) { doRescaleRatio = _doRescaleRatio; @@ -4624,7 +4635,7 @@ bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty std::cout << "Size of genome_maf_smoothed for fitting:\t" << genome_maf_smoothed.size() << "\t\% of full:\t" << (float)genome_maf_smoothed.size() / genome_maf_smoothed_full.size()<< std::endl; auto start = std::chrono::high_resolution_clock::now(); - double bestL = sampleGMM.fitPredict(tau, alpha, genome_ratio_smoothed, genome_maf_smoothed); + double bestL = sampleGMM.fitPredict(tau, alpha, genome_ratio_smoothed, genome_maf_smoothed, maxIterGMM); auto stop = std::chrono::high_resolution_clock::now(); auto duration = std::chrono::duration_cast(stop - start); #pragma omp critical diff --git a/src/GenomeCopyNumber.h b/src/GenomeCopyNumber.h index c12ba15..24b5c39 100644 --- a/src/GenomeCopyNumber.h +++ b/src/GenomeCopyNumber.h @@ -132,6 +132,7 @@ class GenomeCopyNumber void setDataSubsamplingRateInPuritySearch(int dataSubsamplingRateInPuritySearch); void setDataSubsamplingRateInPloidyEvaluation(int dataSubsamplingRateInPloidyEvaluation); void setDoRescaleRatio(bool doRescaleRatio); + void setMaxIterGMM(int maxIterGMM); int findWinNumber(int position, std::string myName, std::string const& matefile); void setWESanalysis(bool WESgiven); @@ -143,6 +144,7 @@ class GenomeCopyNumber bool isMappUsed(); int getDataSubsamplingRateInPuritySearch(); int getDataSubsamplingRateInPloidyEvaluation(); + int getMaxIterGMM(); // Added by Gara float findMaximumPeak(std::vector total_ratio); @@ -171,9 +173,12 @@ class GenomeCopyNumber bool isRatioLogged_; void fillMyHash(std::string const& mateFileName , std::string const& inputFormat, std::string const& matesOrientation, int windowSize, int step, std::string targetBed = ""); + int dataSubsamplingRateInPuritySearch; int dataSubsamplingRateInPloidyEvaluation; bool doRescaleRatio; + int maxIterGMM; + int windowSize_; int step_; long totalNumberOfPairs_; diff --git a/src/GenomeGMM.cpp b/src/GenomeGMM.cpp index c8ef4ff..eb74418 100644 --- a/src/GenomeGMM.cpp +++ b/src/GenomeGMM.cpp @@ -291,16 +291,9 @@ double GenomeGMM::computeLoss(int n) return likelihood; } -double GenomeGMM::fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf) +double GenomeGMM::fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf, int maxIterGMM) { - // TMP - #ifdef CLUSTER - ConfigFile cf("/cluster/home/kzaitse/custom_configs/freec_configs/meta-config.txt"); - #else - ConfigFile cf("/local/home/kzaitse/lab/custom_configs/freec_configs/meta-config.txt"); - #endif // !CLUSTER - int maxIter = (int)cf.Value("gmm", "maxIter", 1); - initialiseGMMParameters(1, maxIter, 2000, 1.0e-7, 1, false, 0.0, 0.01, 0.0, 0.015); + initialiseGMMParameters(1, maxIterGMM, 1000, 1.0e-7, 1, false, 0.0, 0.01, 0.0, 0.015); if (noise_ == 1) { expected_ratio_.push_back(1.0); diff --git a/src/GenomeGMM.h b/src/GenomeGMM.h index c459f27..52690e1 100644 --- a/src/GenomeGMM.h +++ b/src/GenomeGMM.h @@ -39,7 +39,7 @@ class GenomeGMM { double initialiseWeight(); std::vector calculateMarginalResponsabilities(int n); double computeLoss(int n); - double fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf); + double fitPredict(int tau, float alpha, const std::vector& ratio, const std::vector& maf, int maxIterGMM); // Get methods diff --git a/src/bayes_opt.cpp b/src/bayes_opt.cpp index 98b6b97..204379e 100644 --- a/src/bayes_opt.cpp +++ b/src/bayes_opt.cpp @@ -122,7 +122,7 @@ void misc_eval(GenomeCopyNumber genomeCopyNumber, int tau, double alpha) std::map> findBestPurity(GenomeCopyNumber &sampleCopyNumber, std::vector ploidies, ConfigFile &cf, std::string outputDir) { - int optimObjectiveCalls = (int)cf.Value("bayesopt", "optimObjectiveCalls", 1); + int optimObjectiveCalls = (int)cf.Value("bayesopt", "optimObjectiveCalls", 7); double kernelNoise = (double)cf.Value("bayesopt", "kernelNoise", 1e-10); Params::stop_maxiterations::set_iterations(optimObjectiveCalls); Params::kernel::set_noise(kernelNoise); @@ -210,8 +210,6 @@ std::map> findBestPurity(GenomeCopyNumber &sample } } - std::cout << "DIFF with TRUE purity:\t" << abs(truePurity - best_purity) << std::endl; - best_result.insert({best_tau, std::make_pair(best_score, best_purity)}); return best_result; } diff --git a/src/main.cpp b/src/main.cpp index 73f54af..8e2906e 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -821,8 +821,9 @@ int main(int argc, char *argv[]) makingPileup = true; } - int dataSubsamplingRateInPuritySearch = (int)cf.Value("bayesopt","dataSubsamplingRateInPuritySearch",1000); - int dataSubsamplingRateInPloidyEvaluation = (int)cf.Value("bayesopt","dataSubsamplingRateInPloidyEvaluation",50); + int dataSubsamplingRateInPuritySearch = (int)cf.Value("bayesopt","dataSubsamplingRateInPuritySearch",700); + int dataSubsamplingRateInPloidyEvaluation = (int)cf.Value("bayesopt","dataSubsamplingRateInPloidyEvaluation",2); + int maxIterGMM = (int)cf.Value("gmm","maxIter",8); bool doRescaleRatio = (std::string)cf.Value("bayesopt","doRescaleRatio","true") == "true" ? true : false; GenomeCopyNumber sampleCopyNumber; @@ -835,6 +836,7 @@ int main(int argc, char *argv[]) sampleCopyNumber.setIfLogged(logLogNorm); sampleCopyNumber.setDataSubsamplingRateInPuritySearch(dataSubsamplingRateInPuritySearch); sampleCopyNumber.setDataSubsamplingRateInPloidyEvaluation(dataSubsamplingRateInPloidyEvaluation); + sampleCopyNumber.setMaxIterGMM(maxIterGMM); sampleCopyNumber.setDoRescaleRatio(doRescaleRatio); GenomeCopyNumber controlCopyNumber; From 304e52b66e511492813a9247628e04a7ab940756 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Fri, 9 Sep 2022 16:24:48 +0200 Subject: [PATCH 6/7] fix: downscale final score --- src/GenomeCopyNumber.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp index 4835615..620b4c9 100644 --- a/src/GenomeCopyNumber.cpp +++ b/src/GenomeCopyNumber.cpp @@ -4663,6 +4663,8 @@ bool take_subsample_flag, int take_each_nth_element_for_gmm_fit, bool usePenalty } cout << "PENALTY with tau/alpha:\t" << tau << " / " << alpha << "\t-\t" << penalty << endl; double finalScore = (bestL - penalty); + double scoreDownscalingCoef = 1e-5; + finalScore = finalScore * scoreDownscalingCoef; return finalScore; } From 2d8bfd4522b706e2400637d90f5f4e12ab090ce4 Mon Sep 17 00:00:00 2001 From: kirilllzaitsev Date: Fri, 9 Sep 2022 16:25:19 +0200 Subject: [PATCH 7/7] chore:tweak hyperparams --- src/GenomeCopyNumber.h | 2 +- src/bayes_opt.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/GenomeCopyNumber.h b/src/GenomeCopyNumber.h index 24b5c39..5c1ba37 100644 --- a/src/GenomeCopyNumber.h +++ b/src/GenomeCopyNumber.h @@ -208,7 +208,7 @@ class GenomeCopyNumber int N, float threshold_empty = 5e-3, float threshold_noise = 0.1, - int C = 7500); + int C = 1500); }; #endif diff --git a/src/bayes_opt.cpp b/src/bayes_opt.cpp index 204379e..a0cda4c 100644 --- a/src/bayes_opt.cpp +++ b/src/bayes_opt.cpp @@ -33,7 +33,7 @@ struct Params struct acqui_ei : public defaults::acqui_ei { - BO_PARAM(double, jitter, 0.05); + BO_PARAM(double, jitter, 0.01); }; struct init_randomsampling