SPG-group · abiddanda54gene · Apr 8, 2022 · Apr 8, 2022 · Apr 8, 2022 · Apr 8, 2022
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+*.o
+bin/
+obj/
+sandbox/
diff --git a/README.md b/README.md
@@ -1,2 +1,46 @@
 # switchError
 Compute switch error rates
+
+This code was written by Olivier Delaneau with build environment and documentation contributions from Arjun Biddanda.
+
+## Building the executable
+
+The environment to build the software can be conducted by `conda env create -f env.yaml`. You can then subsequently run `conda activate switchError` and `make`, which should build the executable for you in `bin/switchError`.
+
+## Input File Definitions
+
+* "--gen": BCF formatted file of genotyped individuals [required]
+* "--hap": BCF formatted file of individuals with estimated haplotypes [required] 
+* "--fam": PLINK formatted FAM file for evaluating IDs 
+* "--reg": BED-formatted region string for evaluating switch error rates  [required] 
+* "--ps": Phase set information (more information [here](http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#readaware))
+* "--out": output prefix, the outputfiles have extensions `*.iser`, `*.vser`,`*.mser.gz`  [required]
+* "--maf": minor allele frequency cutoff
+
+## Output File Definitions
+
+1. `*.iser`
+
+The columns in order are:
+  * individual index
+  * individual name
+  * number of mendel errors
+  * number of opportunities for mendel errors
+  * number of typing errors
+  * number of opportunities for typing errors
+  * number of switch errors 
+  * number of opportunities for switch errors
+
+2. `*.vser`
+  * variant-level index
+  * position of variant
+  * minor allele count
+  * minor allele frequency 
+  * number of mendel errors
+  * number of opportunities for mendel errors
+  * number of typing errors
+  * number of opportunities for typing errors
+  * number of switch errors 
+  * number of opportunities for switch errors
+
+Across both settings, we largely want to look at how to use the last two columns and their distribution across individuals. 
diff --git a/bin/placeholder.txt b/bin/placeholder.txt
diff --git a/bin/swithError b/bin/swithError
diff --git a/env.yaml b/env.yaml
@@ -0,0 +1,16 @@
+name: switchError
+channels:
+  - conda-forge
+  - bioconda
+  - hcc
+dependencies:
+  - gxx
+  - libstdcxx-ng
+  - boost=1.75.0
+  - automake
+  - cmake
+  - htslib
+  - r-mathlib
+  - libzlib
+  - git
+
diff --git a/makefile b/makefile
@@ -1,12 +1,12 @@
 ##########################################
 # SET CORRECTLY THESE 6 PATHS TO COMPILE #
 ##########################################
-BOOST_INC=
-BOOST_LIB=
-RMATH_INC=
-RMATH_LIB=
-HTSLD_INC=
-HTSLD_LIB=
+BOOST_INC=$(CONDA_PREFIX)/include
+BOOST_LIB=$(CONDA_PREFIX)/lib
+RMATH_INC=$(CONDA_PREFIX)/include
+RMATH_LIB=$(CONDA_PREFIX)/lib
+HTSLD_INC=$(CONDA_PREFIX)/include
+HTSLD_LIB=$(CONDA_PREFIX)/lib
 
 #COMPILER MODE C++11
 CXX=g++ -std=c++0x
@@ -17,46 +17,26 @@ CXXFLAG_DBG=-g
 CXXFLAG_WRN=-Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter
 
 #BASE LIBRARIES
-LIB_FLAGS=-lz -lbz2 -lm -lpthread -llzma
+LIB_FLAGS=-lz -lbz2 -lm -lpthread -llzma  
 
 #FILE LISTS
-BFILE=bin/swithError
+BFILE=bin/switchError
 HFILE=$(shell find src -name *.h)
 TFILE=$(shell find lib -name *.h)
 CFILE=$(shell find src -name *.cpp)
 OFILE=$(shell for file in `find src -name *.cpp`; do echo obj/$$(basename $$file .cpp).o; done)
 VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
 
-#DEFAULT VERSION (I.E. UNIGE DESKTOP RELEASE VERSION)
+#DEFAULT VERSION 
 all: desktop
 
 #UNIGE DESKTOP RELEASE VERSION
-desktop: RMATH_INC=$(HOME)/Tools/R-3.5.1/src/include
-desktop: RMATH_LIB=$(HOME)/Tools/R-3.5.1/src/nmath/standalone
-desktop: HTSLD_INC=$(HOME)/Tools/htslib-1.9
-desktop: HTSLD_LIB=$(HOME)/Tools/htslib-1.9
-desktop: BOOST_INC=/usr/include
-desktop: BOOST_LIB=/usr/lib/x86_64-linux-gnu
 desktop: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)
 desktop: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)
-desktop: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a
+desktop: LIB_FILES=-L$(RMATH_LIB)/ -lRmath  -lboost_iostreams -lboost_program_options -lhts
 desktop: LDFLAG=$(CXXFLAG_REL)
 desktop: $(BFILE)
 
-#UNIL SERVER RELEASE VERSION
-dcb2: LIB_FLAGS=-lz -lbz2 -lm -lpthread -lcurl -lcrypto -lssl -llzma
-dcb2: RMATH_INC=/software/R/3.4.2/include
-dcb2: RMATH_LIB=/software/R/3.4.2/lib64
-dcb2: HTSLD_INC=/home/oldelan/lib/htslib-1.7
-dcb2: HTSLD_LIB=/home/oldelan/lib/htslib-1.7
-dcb2: BOOST_INC=/software/include
-dcb2: BOOST_LIB=/software/lib64
-dcb2: CXXFLAG=$(CXXFLAG_REL)
-dcb2: IFLAG=-Ilib -Ilib/OTools -I$(HTSLD_INC) -I$(BOOST_INC) -I$(RMATH_INC)
-dcb2: LIB_FILES=$(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a
-dcb2: LDFLAG=$(CXXFLAG_REL)
-dcb2: $(BFILE)
-
 
 #COMPILATION RULES
 $(BFILE): $(OFILE)

diff --git a/obj/data_base.o b/obj/data_base.o
diff --git a/obj/data_mendel.o b/obj/data_mendel.o
diff --git a/obj/data_read.o b/obj/data_read.o
diff --git a/obj/data_switch.o b/obj/data_switch.o
diff --git a/obj/data_write.o b/obj/data_write.o
diff --git a/obj/placeholder.txt b/obj/placeholder.txt
diff --git a/obj/switchError.o b/obj/switchError.o
diff --git a/src/data_read.cpp b/src/data_read.cpp
@@ -22,7 +22,7 @@ void data::readPedigrees(string fped) {
 			switch (type) {
 				case 2: n_tri ++; break;
 				case 1: n_duo ++; break;
-				default: n_tri ++; break;
+				default: n_unr ++; break;
 			}
 		}
 	}