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Fix: unmapped reads now pushed to end of coordinate-sorted BAM
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2011-09-28 derekFix: unmapped reads now pushed to end of coordinate...
2011-09-27 derekFixed typo in error messages
2011-09-27 Derek BarnettMerge pull request #16 from gabeiscoding/patch-2
2011-09-23 gabeiscodingIn standard indexed BAM files with with sparce coverage...
2011-09-10 derekMinor cleanup
2011-09-09 derekRemoved unnecessary peek-and-rewind behavior in BamMult...
2011-09-09 derekRemoved 'core mode' concept from BamMultiReader internals
2011-09-08 Derek BarnettMerge pull request #15 from gabeiscoding/patch-1
2011-09-08 gabeiscodingBug discovered. The chunkStop was not being read from...
2011-09-02 derekAdded support for "-" as indicator for stdin/stdout
2011-09-02 derekAdded "isSingleton" property to filter tool
2011-07-27 derekImplemented binary search through bins in BAI
2011-07-06 derekAdded a -minMQ (minimum map quality) option to ResolveTool
2011-06-28 Derek BarnettMerge pull request #13 from alecchap/master
2011-06-28 derekAdded unique-alignment checks for ResolveTool
2011-06-28 Alec ChapmanFix Visual Studio compiler errors.
2011-06-23 derekFixed -fPIC issue for CentOS users.
2011-06-17 derekRemoved pessimistic warnings when jumping to regions...
2011-06-17 derekAdded re-calculation of BamAlignment's BinID during
2011-06-14 derekImplemented better coupling of unmapped reads with...
2011-06-14 derekFurther fixes for ISIZE-handling in ResolveTool
2011-06-13 derekFixed some signed/unsigned InsertSize bugs in ResolveTool
2011-06-11 derekConvertTool fix: removed extra space in (BAM->FASTA...
2011-06-11 derekCreated 3 modes for ResolveTool: makeStats, markPairs...
2011-06-11 derekCleaned up help formatting & added some string utilities
2011-06-07 derekAdded new ResolveTool - for paired-end resolution....
2011-06-07 derekMinor cleanup to toolkit code formatting.
2011-05-10 derekFixed minimum offset error in BAI jumping
2011-05-05 Derek BarnettMerge pull request #9 from bookest/patch-1
2011-05-05 Christopher Grim'make install' should install bin/bamtools
2011-04-27 derekRemoved debug statements that snuck into last commit
2011-04-27 derekFixed regression bug in index formats. Wasn't properly...
2011-04-22 derekAdditional attempt to force -fPIC on CentOS
2011-04-22 derekModified BamAlignment in attempt to resolve symbol...
2011-04-19 derekBrought API up to compliance with recent SAM Format...
2011-04-05 derekRolled back the BGZF buffer size to the original 64K...
2011-04-05 derekMajor performance boost to startup & random-access...
2011-03-23 derekMajor update to BamTools version 1.0
2011-02-24 derekAttempt to fix SamHeaderVersion compile bug
2011-01-19 derekBug fix in SamHeaderVersion::SetVersion()
2011-01-19 derekMissed bug fix in BamMultiMerger in early commit. Fixed...
2011-01-17 derekAdded ExportHeader command for BamConstants.h
2011-01-17 derekRemoved SamHeaderValidatorPrivate pimpl. No real need...
2011-01-17 derekAdded UNSORTED to BamMultiReader::SortOrder types....
2011-01-13 derekMinor formatting cleanup
2011-01-12 derekMinor update to API version 0.9.3 - addition of SamHead...
2011-01-12 derekAdded BamConstants.h
2011-01-12 derekRemoved explicit keyword from SamHeader-related object...
2011-01-12 derekUpdate to BamTools API 0.9.2 with exposure of SamHeader...
2011-01-12 derekAdded explicit copy ctors to SamHeader data structures
2010-12-24 derekAdded SAM header-handling classes for read/write/validate.
2010-12-24 derekUpdated to 0.9.1
2010-12-24 derekImplemented proper -byname sorting (finally).
2010-12-24 derekAdded static library to build step.
2010-12-22 derekMoved BuildCharData() from BamReader to BamAlignment
2010-12-16 derekFixed: Improper sorting -byname
2010-12-15 derekAdded creation of include/ folder in bamtools root...
2010-12-13 derekMinor formatting cleanup
2010-12-13 derekMade BamAlignment flag queries symmetrical
2010-12-07 derekFixed: handling BamAlignments with limited char data
2010-12-06 derekFixed : improper exit code from FilterTool
2010-12-06 derekFixed: core mode setting for BamMultiReader::Open(...
2010-12-06 derekAdded new RevertTool to the toolkit
2010-12-03 derekFixed: bug in the BamReader::Jump() codepath, specifica...
2010-11-22 derekMoved private implementation API files to internal...
2010-11-22 derekAdded proper import of bamtools version info from CMake
2010-11-22 derekFixed BamRegion bug: previously only checked if refID...
2010-11-19 derekContinued breaking up of monolithic classes: extracted...
2010-11-19 derekExtracted BamReaderPrivate & BamWriterPrivate from...
2010-11-19 derekAdded UTILS_EXPORT macro to classes in BamTools utility...
2010-11-19 derekAdded API_EXPORT macro to classes in BamTools API
2010-11-19 derekRemoved commented (library export) definitions from...
2010-11-19 derekMigrated to CMake build system.
2010-11-18 derekChanged GetNextAlignmentCore() calls to GetNextAlignmen...
2010-11-15 derekMinor formatting cleanup
2010-10-27 derekRemoved more non-standard STL calls from BamIndex.cpp
2010-10-27 derekMerge branch 'master' of git://github.com/ekg/bamtools
2010-10-27 derekRemoved non-standard stl::map method calls
2010-10-27 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31...
2010-10-27 Erik Garrisonclarified no-index behavior in bam multi reader
2010-10-25 derekUpdated BamTools version information.
2010-10-21 DerekMerge branch 'master' of git://github.com/ekg/bamtools
2010-10-21 Erik Garrisonadd index caching mode setter to BamMultiReader
2010-10-21 DerekFixed NoIndexCaching behavior
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats
2010-10-16 Derekmodified/clarified some help & usage messages
2010-10-09 DerekChanged BamAlignment::SupportData from private to public.
2010-10-09 DerekFixed: bug(s) related to empty references and regions.
2010-10-05 DerekMinor formatting, commenting cleanup
2010-10-04 derekAdded tag support in filter tool.
2010-10-04 derekReviewed BAM to YAML conversion contribution (thank...
2010-09-29 Erik Garrisonconvert: cleanup of prior fix, report if no index file...
2010-09-29 Erik Garrisonprior commit caused bug with convert
2010-09-28 Erik Garrisonexposes cigar string data to bamtools filter
2010-09-28 Erik Garrisonadded reader.Open checks to a number of tools
2010-09-28 Chase MillerAdded Yaml for outputing BamAlignments.
2010-09-28 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31...
2010-09-23 DerekFixed lack of reverse complemented output in BAM -...
2010-09-23 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31...
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