Changes

iSAAC-01.15.04.01
* SAAC-795 Assertion failure if input bam read names are shorter than 8 characters

iSAAC-01.15.03.31
* SAAC-793 Assertion failure in gap realigner when deletion pushes a section of the read past the contig end
* SAAC-792 unit tests fail due to varying order of initialization

iSAAC-01.15.03.19
* SAAC-787 Combining two bcl-bgzf flowcells in one run causes a failure

iSAAC-01.15.03.12
* SAAC-786 Bam parsing fails on secondary alignments

iSAAC-01.15.02.08
* SAAC-778 y*,n*,y* results in missing alignment stats for read 2

iSAAC-01.15.01.28
* SAAC-726 inefficient memory usage in fastq match finding

iSAAC-01.14.12.05
* SAAC-760 iSAAC TLEN is off by one comparing to BWA 0.7.10-r789 TLEN

iSAAC-01.14.11.27
* SAAC-754 occasionally garbled output bam sections in when bam is used as input

iSAAC-01.14.11.11
* SAAC-746 iSAAC fails to fully decompress bcl-bgzf files

iSAAC-01.14.11.07
* SAAC-742 iSAAC fails to parse fastq containing text after the + separator
* SAAC-741 iSAAC fails parsing fastq.gz with: When no bytes come out of decompressor expecting the input stream to be over

iSAAC-01.14.09.11
* SAAC-728 gap realignment changes clipping so that read part is outside end of the contig

iSAAC-01.14.08.28
* SAAC-723 Change the license to the BSD 2-Clause License
* SAAC-724 iSAAC fails to load xsl template due to a corrupt path

iSAAC-01.14.07.25
* SAAC-714 Allow custom-formatting bam read groups PU field

iSAAC-01.14.07.17
* SAAC-707 multiple empty blocks in fastq.gz result in data not being read

iSAAC-01.14.07.14
* SAAC-704 Insufficient capacity in cycleNumbers_ when non-barcoded data is mixed with barcoded flowcell

iSAAC-01.14.06.18
* SAAC-694 single-ended input bam with one r2 record makes iSAAC fail.

iSAAC-01.14.05.12
* SAAC-680 support for NextSeq bcl and bcl-gz layouts

iSAAC-01.14.05.01
* SAAC-671 Segfault in Match finding on multilane barcoded bcl-bgzf data

iSAAC-01.14.04.17
* SAAC-670 Alignment reports misrepresent reads when use-bases-mask masks out index read

iSAAC-01.14.04.11
* SAAC-668 control fastq and bam tile allocation from command line

iSAAC-01.14.04.09
* SAAC-667 Allow fastq with 0-length reads

iSAAC-01.14.04.08
* SAAC-665 github-8 Configure command must be run twice in order to succeed

iSAAC-01.14.04.04
* SAAC-663 low %align and corrupt output bam when --use-bases-mask forces longer read length than is available in input bam
* SAAC-664 gcc 4.4 compatibility

iSAAC-01.14.04.01
* SAAC-662 configure --static detects dynamic libraries instead of static ones
* SAAC-661 github-7 link to librt
* SAAC-660 github-6 isaac seems to run out of memory in the findNeighbors step

iSAAC-01.14.03.20
* SAAC-657 allow for non-casava bam read names

iSAAC-01.14.03.12
* SAAC-655 boost compilation fails on cygwin due to missing libbz.h
* SAAC-654 github-4 Rev boost libraries (compilation error)
    
iSAAC-01.14.03.11
* SAAC-653 Produce md5 checksum for bam files

iSAAC-01.14.03.06
* SAAC-652 2x75 from bam runs out of memory in match selection

iSAAC-01.14.02.18
* SAAC-649 github-3 iSAAC compilation fails with 'cannot bind bitfield' error on gcc 4.6

iSAAC-01.14.02.10
* SAAC-644 --use-bases-mask y*,n* on bam with paired data produces pile of NNNNN reads in the output
* SAAC-643 --description command line option to store value in iSAAC @PG DS header line tag
* SAAC-642 --help-defaults to produce tab-delimited list of command-line options and their default values

iSAAC-01.14.02.06
* SAAC-639 boost is not built with gcc specified by CXX
* SAAC-638 cmake search for cppunit/Test.h fails on centos 6
* SAAC-636 print command line help orderd by option long name

iSAAC-01.14.02.05
* SAAC-518 confusing failures when --use-bases-mask forces more cycles than there is in the read
* SAAC-635 'Unknown' barcode specification in sample sheet causes failure
* SAAC-538 Empty sample sheet causes confusing segfault
* SAAC-580 bam input temporary files are not cleaned up by --cleanup-intermediary yes

iSAAC-01.14.02.04
* SAAC-634 _S_create_c_locale name not valid when running static builds on el5

iSAAC-01.14.02.02
* SAAC-632 module file name resolution in CYGWIN

iSAAC-01.14.02.01
* SAAC-629 support movable installation

iSAAC-01.14.01.30
* SAAC-630 Bam header contains read groups for lanes that don't have the sample loaded

iSAAC-01.14.01.27
* SAAC-599 ignore supplementary alignments when reading from bam

iSAAC-01.14.01.23
* SAAC-628 iSAAC crashes without an explanation when no tiles are present in a lane from RunInfo.xml
* SAAC-627 libxml2 introduces broken dependency on libiconv on Windows 8

iSAAC-01.14.01.16
* SAAC-625 Command line option to force per-tile tls

iSAAC-01.14.01.13
* SAAC-623 bad_alloc with 2x150 and tiles over 6M clusters in MatchFinder

iSAAC-01.13.12.21
* SAAC-619 --clip-overlapping corrupts NM tag

iSAAC-01.13.12.20
* SAAC-618 bcl-bgzf Lanes 3 and 4 are not present in iSAAC output
* SAAC-611 Memory conrol failure when tiles are filtered with bcl-bgzf data
* SAAC-610 Cygwin compatibility

iSAAC-01.13.12.09
* SAAC-608 Support for flowcell .locs file
* SAAC-519 Support for bcl.bgzf

iSAAC-01.13.12.08
* SAAC-609 Crash when mix of single-ended and paired flowcells is used

iSAAC-01.13.12.04
* SAAC-606 All clusters have same coordinates when .locs files are used

iSAAC-01.13.11.20
* SAAC-602 --keep-unaligned front breaks bam generation

iSAAC-01.13.11.12
* SAAC-537 Support 2x250 data with iSAAC defaults.

iSAAC-01.13.11.07
* SAAC-598 support user-defined number of lanes in fastq base calls folder
* SAAC-589 --seeds all option to automatically generate seed at every base of the read
* SAAC-593 MatchSelector takes forever when --start-from MatchSelector is used 

iSAAC-01.13.10.21
* SAAC-592 Debug GLIBC out of bounds access failures
* SAAC-591 failure to uncompress read2 fastq.gz file

iSAAC-01.13.10.14
* SAAC-586 TLEN must be set to 0 for singletons the same way as for single reads
* SAAC-585 all reads get misplaced if the hardware parallelization changes between MatchFinder and MatchSelector

iSAAC-01.13.10.07
* SAAC-583 static builds don't work on el6
* SAAC-581 Support .locs position files
* SAAC-582 execution hangs after exceptions in match selector

iSAAC-01.13.09.26
* SAAC-578 Bcl file path is not available in the error message when bcl.gz is corrupt.
* SAAC-579 Allow for multiple fastq.gz input files to be concatenated together
* SAAC-577 MatchSelector failure when same bam file used twice as -b parameter

iSAAC-01.13.09.17
* SAAC-575 Compilation fails with gcc 4.6
* SAAC-572 Don't fail on barcodes longer than 21 bases if demultiplexing is not required.

iSAAC-01.13.09.13
* SAAC-573 Bin index in bam records different from what samtools would have assigned.
* SAAC-574 MatchSelector hangs if more than one bam file used as input.
* SAAC-569 Bam generation hangs when one of the threads fails due to an exception

iSAAC-01.13.09.09
* SAAC-567 When running from bam, last portion of unpaired reads turns into NNNNNN
* SAAC-568 --tls argument results in different shadow rescue range than when same template is computed from data
* SAAC-566 realignment places macthing part of CIGAR outside the reference contig end
* SAAC-562 Unsafe zlib memory management

iSAAC-01.13.07.25
* SAAC-561 Ensure proper pair flag is set only in reads of pairs that are within dominant template statistics

iSAAC-01.13.07.11
* SAAC-557 --pessimistic-mapq option to control whehter to use min or max SM,AS as MAPQ

iSAAC-01.13.07.03
* SAAC-553 overlap clipper leaves insertions and deletions on the right side of the clipped read
* SAAC-552 Legacy --variable-fastq-read-length option does not work

iSAAC-01.13.06.27
* SAAC-546 Rewrite user guide in markdown

iSAAC-01.13.06.24
* SAAC-545 Cigar with 0M formed as result of realignment near the bin border
* SAAC-542 allow multiple flowcells to be present in input bam file

iSAAC-01.13.06.21
* SAAC-543 Overlapping ends clipper causes crash on chimeric pairs
    
iSAAC-01.13.06.20
* SAAC-534 Clipping the overlaps
* SAAC-541 fix the source code github url
* SAAC-540 Remove support for CASAVA integration

iSAAC-01.13.06.19
* SAAC-512 Support bam as input data source
* SAAC-539 iSAAC mismatch plots round to the nearest 1%

iSAAC-01.13.05.29
* SAAC-522 Tabs in iSAAC command line cause broken bam header

iSAAC-01.13.05.23
* SAAC-505 Custom entries to bam file header

iSAAC-01.13.05.09
* SAAC-517 Fastq base quality score range checking is broken
    
iSAAC-01.13.05.08
* SAAC-516 gap realigner clips read ends at the bin border even if contig has bases in the subsequent bin

iSAAC-01.13.05.07
* SAAC-513 ParallelBclMapper threads go bananas if there are more threads than cycles to read
* SAAC-514 gap realigner does not soft-clip the end of the read hanging outside the chromosome
* SAAC-511 unpacked reference fasta is formatted differently even if the original is a single multi-contig file
* SAAC-509 Have an option to preserve all reference contigs in bam header
* SAAC-508 isaac-unpack-reference prints bunch of warnings and fails to produce mask files without an explanation.

iSAAC-01.13.04.29
* SAAC-506 fastq with incorrect quality bases (all Q64) does not fail until the end where it crashes in bam 90.2bchkmnopst-statistics generation
* SAAC-503 skipping contigs on reordered reference produces broken bam

iSAAC-01.13.04.15
* SAAC-502 iSAAC attempts to load clocs files regardless of --bam-exclude-tags setting

iSAAC-01.13.04.12
* SAAC-440 --bam-exclude-tags: User control over which tags go into BAM
* SAAC-346 Store cluster position information in bam

iSAAC-01.13.04.04
* SAAC-500 isaac-reorder-reference duplicates Contig entries in the sorted-reference.xml

iSAAC-01.13.03.31
* SAAC-499 Use 16-mers as seeds
* SAAC-494 Use 64-mers for seeds

iSAAC-01.13.03.27
* SAAC-497 TotalKmers is incorrect in sorted-reference.xml
* SAAC-496 extractNeibhors breaks on toomanymatch kmers
* SAAC-465 Improve performance on large numbers of reference contigs (millions of contigs) 
* SAAC-488 Keep the expected size of match lists around 4 Gb when processing fastq
* SAAC-474 MatchDistribution does not account for matches that have over 2 repeat positions

iSAAC-01.13.03.21
* SAAC-493 Semialigned shadows that are too bad for rescuing cause downgraded alignment scores
* SAAC-156 24 thread GA run for 8x120 tiles 96 samples per lane takes 20 minutes to dump the MatchSelector statistics
* SAAC-492 Trace more details for bcl failures

iSAAC-01.13.03.20
* SAAC-491 Dual barcode sample sheet fails with barcode length mismatch error

iSAAC-01.13.03.19
* SAAC-490 Realignment of left-clipped read against insertion produces reads out of order in the bam file

iSAAC-01.13.03.18
* SAAC-457 Prevent sample sheet having different barcode length than the data
* SAAC-487 Store Build.xml using libxml instead boost ptree
* SAAC-486 Shadow rescuing fails to rediscover pairs outside the dominant template length which results in rejecting or scoring low long deletions
* SAAC-485 flank mismatches computed improperly prevent accepting long indels

iSAAC-01.13.03.14
* SAAC-481 Failure in DemultiplexingStats when total number of tiles goes over 1000
* SAAC-483 Show %Align for non-unique alignments as well
* SAAC-482 port SAAC-476 (libxml installation fixes) to SAAC-00.12.10.03_branch

iSAAC-01.13.03.13
* SAAC-480 rename sortedReferenceXml to sortedReferenceMetadata
* SAAC-479 Excessive amount of debug traces during reference xml loading
* SAAC-475 use libxml to work with sorted reference metadata

iSAAC-01.13.03.12
* SAAC-478 iSAAC-01.13.03.06 elevated memory requirement in MatchSelector
* SAAC-477 --realign-gaps no fails in bam generation

iSAAC-01.13.03.10
* SAAC-476 nanohttp warnings when linking
* SAAC-473 Have an option to cleanup temporary input files of completed stages
* SAAC-472 Read lengths mismatch between lanes of the same flowcell FastqFlowcellInfo(H05A2ADXX,100:101,[2 ]) vs FastqFlowcellInfo(H05A2ADXX,101:101,[1 ])

iSAAC-01.13.03.07
* SAAC-471 extremely high number of improperly scored misplaced reads

iSAAC-01.13.03.06
* SAAC-469 smith-waterman misplaces gapped alignment which don't begin with deletion
* SAAC-470 alignment score too high for a repeat of 2 in MatchSelector
* SAAC-468 FragmentBuilder::consolidateDuplicateFragments error: attempt to dereference a past-the-end iterator.
* SAAC-467 SimpleIndelAligner::alignSimpleInsertion error: attempt to dereference a past-the-end iterator
* SAAC-462 iSAAC_LOG_LEVEL:=1 breaks reference sorting

iSAAC-01.13.03.04
* SAAC-154 Ensure reference specifications don't conflict within the project/sample
* SAAC-321 Have an option to share gaps for realignment across multiple samples
* SAAC-448 Have an option to force more neighboring gaps for realignment
* SAAC-456 In case of multiple realignments, avoid wasting CIGAR storage by keeping only last realignment CIGAR
* SAAC-459 Long insertion reduces mismatches but misplaces the entire read
* SAAC-458 Make the assumptions about how many gaps are introduces by realignment configurable 

iSAAC-01.13.02.22
* SAAC-464 Xml storage for aligner state is too slow, use boost text archive instead
* SAAC-463 Fasta files over 4 gigabytes long cause isaac-align to crash
* SAAC-461 Linux default memory fastbins cause too much virtual memory being wasted in bam generation

iSAAC-01.13.02.19
* SAAC-434 Empty FASTQ file will cause iSAAC align fail 
* SAAC-455 Don't accept simple indels with too many mismatches around the gap
* SAAC-454 Reference clipping and alignment-independent clipping breaks simple gap aligner
* SAAC-453 --package-tgz produces file without processor specification in the name
* SAAC-452 configure attempts to create target folders if they don't exist

iSAAC-01.13.02.01
* SAAC-451 debug statement breaks alignment report generation
* SAAC-450 ram over 256G is not being used for fastq match finding
* SAAC-445 use ISAAC_HOME environment variable at runtime to override the --prefix value supplied during package generation

iSAAC-01.13.01.31
* SAAC-449 Fastq reading is broken in paired data

iSAAC-01.13.01.30
* SAAC-424 Speed up alignments of high repeats by terminating the template building early
* SAAC-447 parallelize fastq parsing and decompression

iSAAC-01.13.01.28
* SAAC-446 Alignment-independent clipping (quality masking, adapter trimming) prevents realignment
* SAAC-411 Allow realignment for reads with downgraded alignment scores
* SAAC-84 Match finder stats are missing counts for NoMatchSeeds and TooManyRepeatSeeds
* SAAC-443 --default-adapters AGATCGGAAGAGC*,*GCTCTTCCGATCT breaks SimpleIndelAligner
* SAAC-442 Gap realigner fails to compact CIGAR with 2x250 RNA data

iSAAC-01.13.01.15
* SAAC-441 development trace 'using bcmdl :-(' clutters bam generation log
* SAAC-273 keep duplicates without marking them in bam file
* SAAC-437 Duplicates within sample are not detected if they are on different lanes

iSAAC-01.13.01.10
* SAAC-428 Integrate base quality score binning into iSAAC
* SAAC-354 Make real barcodes available in Bam file

iSAAC-01.13.01.04
* SAAC-433 Cleaner error reporting
* SAAC-431 Single-ended downgraded alignments still have AS and SM tags

iSAAC-01.12.12.17
* SAAC-427 Deletion gaps are associated with wrong samples in multi-sample data
* SAAC-426 Use std::ofstream instead of filtering stream in Bam generation
* SAAC-425 When multiple bam files are produced some of them are missing bgzf footer

iSAAC-01.12.12.14
* SAAC-420 Confusing error message for duplicate command-line arguments
* SAAC-422 Both scores must be either present or missing. failure with --dodgy-alignment-score Unaligned
* SAAC-423 orBits fails with locale error during reference unpacking on some systems

iSAAC-01.12.12.12
* SAAC-418 Produce WIG annotations for unique, toomanymatch and neighbor-having kmers in the reference
* SAAC-300 isaac-sort-reference fails if the path to .fa file is not absolute
* SAAC-419 Some kmers are not marked as having neighbors in the reference
* SAAC-417 toomanymatch reference kmers are not accounting for reverse complements
* SAAC-404 2x250 data with 7M clusters per tile requires over 86 gigabytes of RAM

iSAAC-01.12.12.06
* SAAC-410 single-ended bam fails picard validation
* SAAC-407 assertion (clusterInfo.isBarcodeSet()) failed ... Barcodes must be resolved at this point

iSAAC-01.12.12.05
* SAAC-413 Apply the Illumina Open Source License 1
* SAAC-209 original read numbers need to be visible in reports
* SAAC-338 Support fastq for single-ended data
    
iSAAC-01.12.12.04
* SAAC-415 M5 calculated improperly

iSAAC-01.12.12.03
* SAAC-412 Error message is confusing when use-bases-mask 'y' has value bigger than read length in fastq
* SAAC-353 Support varying read length in FASTQ
* SAAC-409 Stop producing bin index files.

iSAAC-01.12.11.23
* SAAC-408 Gap realigner randomly decided not to realign some reads between to different runs of MatchSelector on the same data using the same command line
    
iSAAC-01.12.11.21
* SAAC-406 *** glibc detected *** /export/scratch/rpetrovski/ISAAC_INSTALL/SAAC00404/iSAAC-SAAC00404.12.11.20/bin/isaac-align: munmap_chunk(): invalid pointer: 0x00002ab1628a0010 ***

iSAAC-01.12.11.20
* SAAC-403 Allow for number specification in --dodgy-alignment-score
* SAAC-405 Assertion failure: alignment score too high for a repeat of 2

iSAAC-01.12.11.19
* SAAC-401 Long insertions are not detected when anchor seeds overlap
* SAAC-402 Consolidation of perfect ungapped alignment with bad gapped alignment results in high scored misplaced read
* SAAC-396 Use max of SM and AS for MapQ
* SAAC-393 configure reinstalls xml libraries each time it is being executed
* SAAC-394 Shadow diversity cutoff causes overestimated pair alignment scores
* SAAC-391 Treat reference Ns as mismatches for alignment selection
* SAAC-305 Special characters in sample id and project name

iSAAC-01.12.10.31
* SAAC-389 Pf clusters is incorrect in html statistics when reads are too short to have a multiseed pass
* SAAC-390 Reads shorter than 64 bases cause failure during seed loading
* SAAC-387 Two bam files produced the same way differ in the order in which the reads of the same cluster are placed in the file
* SAAC-388 change --clip-semialigned default to on so that GATK does not produce too many conflicting snps

iSAAC-01.12.10.30
* SAAC-228 Medium size gap detection in MatchSelector
* SAAC-387 Two bam files produced the same way differ in the order in which the reads of the same cluster are placed in the file

iSAAC-01.12.10.29
* SAAC-379 GATK fails to read bam file with Reference index 50846067 not found in sequence dictionary or similar
* SAAC-384 Gap realigner does not use long deletion if the read enters it from the right

iSAAC-01.12.10.25
* SAAC-379 GATK fails to read bam file with Reference index 50846067 not found in sequence dictionary or similar
* SAAC-380 Bam Indexer doesn't count the final unmapped reads correctly
* SAAC-375 Blocked memory allocation in BamIndexer
* SAAC-381 Gap realigner fails when read is realigned against multiple insertion gaps starting at the same position
* SAAC-383 Gap realigner fails when trying to apply a gap overlapped by a deletion that already exists in the read
* SAAC-369 Gap realigner introduces a single base insertion and a single base deletion to get rid of one mismatch 

iSAAC-01.12.10.19
* SAAC-378 Rollback SAAC-374 as it increases trio conflicts and high-scored misplaced reads in accuracy validation
* SAAC-377 Failure on bcl files that are exactly 4096x bytes big
* SAAC-351 Off by one in quality trimming

iSAAC-01.12.10.16
* SAAC-373 bandedSmithWaterman crashes on 2x400 data
* SAAC-374 Incorrect scoring of templates where in rescueShadow the shadow aligns to multiple positions as ungapped but gapped aligner turns those alignments into identical ones
* SAAC-372 Reduce MatchSelector memory consumed by tile statistics
* SAAC-341 Make iSAAC filter files detection future-compatible by assuming all RTA >=1.9 has single filter file per tile in lane folder.
* SAAC-370 Log iSAAC version in the log file
* SAAC-368 Gap realigner changes the CIGAR even though the number of mismatches and edit distance stay the same

iSAAC-01.12.10.09
* SAAC-367 --pf-only must discard non-pf clusters instead of keeping them in unaligned data
* SAAC-334 NM gets broken by gap realigner and semialigned clipper

iSAAC-00.12.10.04
* SAAC-363 --repeat-threshold 100 causes boost::numeric::ublas::bad_size failure
* SAAC-364 New defaults for iSAAC Isis compatibility
* SAAC-360 M5 fields in the .bam file header are blank

iSAAC-00.12.10.03
* SAAC-343 Picard Bam validation errors
* SAAC-362 Crash when aligning small number of human tiles against single chr22 
* SAAC-361 set_mempolicy fails with invalid argument 

iSAAC-00.12.10.02
* SAAC-359 Crash during multiplexed bam saving 
* SAAC-358 Crash during bam generation when single-ended data is present
* SAAC-357 vector::_M_range_check during bam generation

iSAAC-00.12.09.27
* SAAC-352 Allow unaligned data to be placed at the end of the BAM file 
* SAAC-349 Parallelise BAM indexing 
* SAAC-356 Unaligned data compression takes many hours.
* SAAC-337 Increase memory access locality for Bam generation
* SAAC-301 faster bam generation
* SAAC-326 gcc 4.7.1 compilation warnings
* SAAC-335 gnuplot 4.6 compatibility 
* SAAC-342 Support for --stats-image-format command line option, gif or none

iSAAC-00.12.09.17
* SAAC-340 Support RTA 1.17 filters file location

iSAAC-00.12.09.14
* SAAC-283 Store MD5 hashes of reference sequences in Bam file 
* SAAC-336 Pull workflow logic out of MatchSelector 
* SAAC-333 Support compressed fastq 
* SAAC-331 Remove config.xml dependency for fastq datasets, discover lanes based on file globbing 
* SAAC-330 Support match selection from fastq 
* SAAC-328 Support match generation from fastq
* SAAC-324 Move tile metadata discovery into match finding 
* SAAC-332 0-quality bcl CGT are not treated the same way as 0-quality A

iSAAC-00.12.08.28
* SAAC-323 Use -rfakeroot when building debian packages
* SAAC-327 --build-type does not work in configure
* SAAC-322 clip-semialigned does not work for single-ended reads

iSAAC-00.12.07.26
* SAAC-317 Heavily clipped rescued shadows of long reads pass badness checking regardless of the number of mismatches they have
* SAAC-320 Short adapters cause alignment bias by accidentally soft clipping bad alignments and making them look good
* SAAC-319 Reverse adapter starting after the read end clips off the entire read in standard protocol 
* SAAC-318 Adapter starting before the read start clips off the entire read in standard protocol
    
iSAAC-00.12.07.25
* SAAC-303 Gap realignment destroys original clipping
* SAAC-294 Semialigned ends soft clipping
* SAAC-292 Bin filtering for bam generation (debug feature)
* SAAC-290 Treat artificially lowererd mapping quality reads separately form real mapq 0 reads
* SAAC-288 Correctly account for disjointed template candidates and rediscovered shadow probabilities
* SAAC-261 Scatter repeat alignments across all candidate locations

iSAAC-00.12.07.24
* SAAC-316 gap realignment sometimes pushes read into the next bin which causes out-of-order reads in the bam file

iSAAC-00.12.07.20
* SAAC-287 Have --pf-only yes as default
* SAAC-300 isaac-sort-reference fails if the path to .fa file is not absolute
* SAAC-298 --gzip-level 0 breaks bam generation
* SAAC-299 Output folder restructuring

iSAAC-00.12.07.09
* SAAC-297 chopped CIGAR in the bam file
* SAAC-296 mismatch plots of multiple flowcells overwrite each other.
* SAAC-295 multiple flowcells of different read lengths (or --use-bases-mask) cause extremely low percent align and totally incorrect bases in the bam data.

iSAAC-00.12.07.03
* SAAC-293 Crash during bam generation when sample sheet with barcodes is used.
* SAAC-291 Bam memory estimation incorrectly fails on the firs bin (unaligned) and does not check the last bin memory requirement

iSAAC-00.12.06.26
* SAAC-263 Trim low quality bases at the end of the read
* SAAC-269 Wrong side of the adaptor gets clipped in standard protocol
* SAAC-264 mismatch cycles incorrectly counted when non-gap-aligned read is soft clipped
* SAAC-286 Store plain sample id instead of project/sample id in BAM RG/SM tag

iSAAC-00.12.06.18
* SAAC-272 Elevated number of gaps in CASAVA sites.txt.gz

iSAAC-00.12.06.15
* SAAC-268 Support for missing bcl and filter files
* SAAC-282 create tools for packing and unpacking sorted reference so that it can be quickly transferred between locations
* SAAC-170 std::runtime_error: locale::facet::_S_create_c_locale name not valid when using static RPM built in UK on amazon cluster compute cloud instances
* SAAC-281 Comments break SampleSheet parser
* SAAC-280 integrate with CASAVA 1.9.0a4

iSAAC-00.12.06.08
* SAAC-279 Support for debian package generation
* SAAC-278 Ubuntu 12.04 LTS compatibility
* SAAC-277 Change adaptor to adapter everywhere
* SAAC-161 Relative --prefix during installation causes alignment report generation failure during the analysis.
* SAAC-224 Support for SQ UR bam tag in reference sorting and bam generation
* SAAC-276 Set minimum cmake requirement in sync with cmake included with the package
* SAAC-170 std::runtime_error: locale::facet::_S_create_c_locale name not valid when using static RPM built in UK on amazon cluster compute cloud instances

iSAAC-00.12.06.07
* SAAC-275 Enforce gcc >= 4.6.1 during installation configuration
* SAAC-274 Allow for installing iSAAC without CASAVA integration
* SAAC-271 integrate with CASAVA 1.9.0a3
* SAAC-270 MiSeq sample sheet Manifests column crashes sample sheet parsing
* SAAC-82 Make sure IO errors are checked in Bgzf code
* SAAC-257 Implement --keep-unaligned to store the pairs that don't align in the bam file
* SAAC-236 Flag duplicates in Bam instead of removing them, make behavior configurable
* SAAC-262 transfer casava genome folder contents into the output
* SAAC-267 Discard clusters that form a pair where both reads align at the same position in the same direction

iSAAC-00.12.05.20
* SAAC-265 Elevated number of trio conflicts with improved alignment scoring data
* SAAC-266 seeds with matches over repeatThreshold are not correctly removed from MatchSelector consideration causing biased pair alignment scores

iSAAC-00.12.05.14
* SAAC-260 MatchSelector segfault due to seed matches going over the repeatThreshold when counted across multiple masks
* SAAC-259 Mapping quality scoring improvements

iSAAC-00.12.05.08
* SAAC-256 Failure when multi-seed can fit less tiles in RAM than the single-seed phase
* SAAC-255 Q1 N is written into Bam instead of any base with quality 1
* SAAC-253 Gap realigner produces a pair of insertion and deletion of an equal size in place of a mismatch

iSAAC-00.12.05.04
* SAAC-251 Gap realigner moves perfectly aligning read by one base
* SAAC-247 GATK 'Adjacent I/D events in read' error
* SAAC-250 Support for single-barcode MiSeq SampleSheet.csv
* SAAC-248 non-zero --neighborhood-size-threshold breaks MatchSelector

iSAAC-00.12.04.27
* SAAC-246 CASAVA interation realigned bam files are not transferred into the output location
* SAAC-245 CASAVA integration notMapped directory crashes transfer of results due to missing Indel folder in it
* SAAC-242 Alignment scores for rescued reads are often overestimated
* SAAC-243 N-containing reads get misplaced
* SAAC-241 0-quality T is written into the bam file instead of N
    
iSAAC-00.12.04.20
* SAAC-238 dos line endings in .fa file result in incorrect count for TotalBases and break alignment.
* SAAC-239 Odd read length results in last base being corrupt (= instead of base letter in samtools view)
* SAAC-240 duplicate locations in fragment lists reduce alignment scores (and % align)
* SAAC-233 Default value for --gap-scoring is missing

iSAAC-00.12.04.11
* SAAC-225 Make gapped alignment penalty configuration available on command line
* SAAC-232 Don't change default CASAVA bin sizes as CNVseg crashes otherwise
* SAAC-231 Transfer Indels folders content into output tree

iSAAC-00.12.04.10
* SAAC-230 Comma after the colum heading in MiSeq sample sheet causes incomprehensible failure message
* SAAC-221 Short indel realignment
* SAAC-227 samtools view -H produces binary zero between last @RG end and first @SQ
* SAAC-226 Generated Reads.idx flowcell names column is empty
* SAAC-223 Show raw mismatch rate in reports
* SAAC-222 Support for non-multiplexed MiSeq sample sheet
* SAAC-152 Implement barcode mismatch statistics reporting
* SAAC-212 special characters in chromosome name break build statistics generation 
* SAAC-219 --start-from Bam results in 0 counts in BuildStats.xml
* SAAC-219 Support filter files location for RTA 1.15 and 1.16.
* SAAC-218 Chromosome names are messed up in BuildStats.xml and Casava duplicate statistics.
* SAAC-217 Rare crash during adaptor trimming
* SAAC-216 Support MiSeq sample sheets
* SAAC-210 adaptor trimming
* SAAC-215 Partial sample sheets cause lanes to be erroneously ignored in processing
* SAAC-214 Blocked memory allocations for TemplateBuilder rescuedPositions_
* SAAC-213 Crash when sample sheet first barcode points to unmapped reference
* SAAC-211 --tls is broken by SAAC-189
* SAAC-208 support non-paired data analysis
* SAAC-207 set default --temp-parallel-save 64 as most of users are running isaac with Temp on isilon at the moment
* SAAC-206 create a tool for changing karyotype ordering of the sorted reference
* SAAC-205 Support chromosome order remapping for bam generation
* SAAC-204 summary barcode 'all' statistics gets into Reads.idx
* SAAC-153 Store barcode string in SM RG tag
* SAAC-203 Allow users to specify casava post-run command
* SAAC-202 make alignment reports navigation tree node names easier to understand
* SAAC-185 command-line switch to enable quality remapping for GATK compatibility
* SAAC-201 Build memory testing may run out of memory
* SAAC-168 Extend command line to supply custom attributes to CASAVA variant calling
* SAAC-200 enable casava gVCF generation
* SAAC-199 duplicate statistics report is missing in generated casava build
* SAAC-198 Match selector incorrectly splits dot-containing sample name into a separate element.
* SAAC-197 avoid running with unlimited memory to prevent failure
* SAAC-196 filter file paths incorrectly detected with RTA 1.11.4
* SAAC-195 iSAAC crashes with -m 27 when more tiles fit in memory during single-seed than multi-seed
* SAAC-189 Allow command-line specification for the shadow aligner scan range.
* SAAC-182 Add BAM indexer for on-the-fly bai file generation
* SAAC-188 ensure isaac works on 32g 8 core machine without fast local disk
* SAAC-193 copy CASAVA sites files into Aligned tree
* SAAC-191 reduce time wasted on pointless gapped alignment attempts
* SAAC-192 incoherent tiles end up breaking grouper pair stats aggregation
* SAAC-184 Accuracy improvements
* SAAC-183 count perfectly matching uniquely aligned fragments in match selector statistics
* SAAC-169 Rename align to isaac and have it installed into /usr/local/bin by default
* SAAC-174 Improve repeat and neighbor match information exchange between MatchFinder and MatchSelector my introducing a 'too-many' reference position
* SAAC-181 Extract meaningful Casava build results files into Aligned folder
* SAAC-178 In singleton/shadow pair shadow does not always follow the singleton in the bam file
* SAAC-171 Increase granularity of CASAVA bins to reduce the minimum amount of time grouper spends on bad bins
* SAAC-179 Avoid crashing if configured seed offsets go outside read boundary.
* SAAC-173 Match finder should generate nomatch matches only at the neighbors matching step
* SAAC-126 BAM generation hangs if one of the threads fails with an exception.
* SAAC-172 make iSAAC rpm depend on casava and gnuplot
* SAAC-166 bam proper pair flag is set for chimeric templates
* SAAC-137 Add the @PG tags in the header of the BAM file
* SAAC-162 Relative --prefix during installation breaks alignment report generation at runtime
* SAAC-167 confusing failure when using use base mask that is incompatible with the nubmer of reads in BaseCalls/config.xml
* SAAC-165 iSAAC must allow processing compressed bcl data
* SAAC-164 Duplicate removal must not cross lane-barcode boundary
* SAAC-163 Integrated CASAVA variant calling
* SAAC-160 Granular control over IO parallelization
* SAAC-157 use fadvise interface to reduce io cache trashing using fadvise for match lists and reference kmer files
* SAAC-139 Implement support for multiple references
* SAAC-116 Multiplexed data support
* SAAC-148 bin files get occasionally corrupted and then Bam generation fails
* SAAC-138 binary 0 separates HD entry from the rest of the text in BAM header
* SAAC-135 Add the @RG tag in the header of the BAM file and the RG field in the alignment section
* SAAC-134 Add the optional field NM (edit distance) to the BAM file
* SAAC-133 Replace the edge-insertions with soft clipping
* SAAC-125 Support multiple flowcells per single analysis in statistics and reports
* SAAC-123 support generation of mismatch statistics images
* SAAC-124 Integrate report generation into alignment execution
* SAAC-122 Create transformation templates for html report
* SAAC-112 Match files fragmentation causes slow data reading on single-disk systems
* SAAC-120 Neighbors search is not done across strands
* SAAC-108 Neighbors finding takes too long
* SAAC-97 The quality scores calculated by the shadow aligner do not take into account multiple matches
* SAAC-114 missing bam AS tag causes grouper to go bad
* SAAC-111 Set the mapq of chimeric templates to the alignment score of the individual fragments
* SAAC-109 Disjoined templates where one mate has a quality less than the mapq threshold should be reported as orphans
* SAAC-110 The log-probability for mismatches is incorrect
* SAAC-107 Add a command line option to control the number of mismatches allowed after gap-alignment
* SAAC 106 Set the mapq to the SM for singletons.
* SAAC-105 Add a command line option to filter the templates based on the mapping quality
* SAAC-53 clusters that fail filtering must be properly flagged in bam
* SAAC-103 Keep a consistent scoring for the individual fragments, regardless of the pairing
* SAAC-101 Add the name of the flow-cell to the temporary match files
* SAAC-100 Implement a faster strategy to select the number of tiles allocated to each pass of the match finding
* SAAC-64 Store individual fragment alignment scores as a BAM optional field SM
* SAAC-38 Mate bin is not set in fragment index which will cause erroneous duplicate removal in edge cases
* SAAC-89 I want to be able to perform CASAVA variant calling on iSAAC BAM
* SAAC-98 Reduce the overhead required to find neighbors
* SAAC-96 non-ACGTN characters in the reference cause alignment position shift
* SAAC-94 Remove the reverse reference from the contigs
* SAAC-95 Always use the forward reference for the shadow aligner
* SAAC-93 Always use the forward reference for the ungapped aligner
* SAAC-96 non-ACGTN characters in the reference cause alignment position shift
* SAAC-92 Always use the forward reference for the gap aligner
* SAAC-91 Add the reverse sequence and the reverse quality in the Read
* SAAC-88 The user should be able to discard the fragments that do not pass the filter
* SAAC-87 Update the command line options to support multiple flow cells
* SAAC-86 Add the flowcell into the BAM fragment id
* SAAC-71 MatchFinder control structures are allocated after the seeds are loaded
* SAAC-72 Parallel seed loading must not use dynamic memory allocations.
* SAAC-83 The fragment list is not resized after consolidation in the match selector
* SAAC-81 Add support for gapped alignment in the shadow aligner
* SAAC-80 Add command-line options to specify the template length statistics
* SAAC-79 Improve the sensitivity of the gapped aligner to allow gaps even with a large number of errors
* SAAC-78 Add debugging functionalities to help understanding the root cause of poor alignments
* SAAC-76 Implement Build memory control
* SAAC-77 The matches are incorrectly sorted, which results into duplicate fragments
* SAAC-75 Mark all the reverse-complement of k-mers with neighbors as habing neighbors
* SAAC-68 Add support for mismatches in the suffix of the seeds
* SAAC-69 Implement MatchSelector memory control
* SAAC-74 Store in the SortedReference.xml file the largest count of positions with the same 16-mer prefix
* SAAC-73 Detect the existence of non-exact neighbors during the exact match finding
* SAAC-67 Add the suffix neighbourhood information into the sorted reference
* SAAC-70 make sure crashes produce meaningful logs and core dumps
* SAAC-57 MatchFinder memory control does not account for foundMatches_
* SAAC-46 Add support for gapped-alignments
* SAAC-61 Implement a mechanism to rescue misaligned pairs
* SAAC-58 Reduce the number of MatchSelector output files
* SAAC-62 Add support for multi-seed on the first pass
* SAAC-59 Implement the orphan aligner
* SAAC-60 empty bins produce corrupt bam files
* SAAC-55 implement Aligner state persistence
* SAAC-48 Unexpected binIndex in the FragmentDispatcher
* SAAC-52 Implement memory control in MatchFinder
* SAAC-51 it should be possible to specify the repeat cutoff threshold for reference sorting
* SAAC-50 Implement memory control in BAM generation
* SAAC-49 Implement multi-seed support
* SAAC-36 Implement a SeedManager
* SAAC-47 parallelMerge memory consumption must be limited
* SAAC-43 Implement summary reporting framework
* SAAC-30 implement PCR duplicate processing and bam generation
* SAAC-33 Add multi-threading to the match selector
* SAAC-29 implement --use-bases-mask in aligner
* SAAC-27 implement regex filtering of lanes and tiles taken from BaseCalls/config.xml
* SAAC-20 Implement the distributed and parallel infrastructure to generate all the sorted reference files
* SAAC-32 Accumulate appropriate level of statistics during seed matching to allow some homogeneity in the size of the alignment bins
* SAAC-31 Produce CIGAR strings instead of the ELAND alignment descriptors
* SAAC-35 Implement a TemplateBuilder component
* SAAC-34 Implement the FragmentBuilder component
* SAAc-24 Add support for reading split sorted reference files into the aligner
* SAAC-22 implement a single-seed, single-end exact aligner
* SAAC-21 Implement a mock-up implementation including the complete user interface for the aligner
* SAAC-16 Implement the mock-up application including the complete interface