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[bamtools.git] / src /
2011-11-28 derekmerge with remoteio branch tree | commitdiff
2011-11-28 derekUpdated CMakeLists.txt files tree | commitdiff
2011-11-28 derekInitial test suite commit tree | commitdiff
2011-11-17 derekBasic Windows implementation tree | commitdiff
2011-11-15 derekRemoved spurious assert tree | commitdiff
2011-11-10 derekUpdated file headers (filename, license, description... tree | commitdiff
2011-11-10 derekAdded generic I/O device to BamIndex side of things tree | commitdiff
2011-11-09 derekAdded FTP support (text-tested, not BAM) tree | commitdiff
2011-11-07 derekImplemented basic TCP support layer tree | commitdiff
2011-10-25 derekOrganized api/internal into subdirs tree | commitdiff
2011-10-17 derekRemoved some debugging 'error string' messages that... tree | commitdiff
2011-10-17 derekRegression fixed: error in BamAlignment tag access... tree | commitdiff
2011-10-16 derekRemoved data duplication in last update to Sam*Dictionaries tree | commitdiff
2011-10-14 derekFixed regression: improper @SQ line ordering in SamHead... tree | commitdiff
2011-10-14 derekRegression fixed: wasn't properly merging from multiple... tree | commitdiff
2011-10-14 derekMinor cleanup in FilterTool tree | commitdiff
2011-10-13 derekAdded GetSoftClips() method to BamAlignment tree | commitdiff
2011-10-12 derekMajor speedup in SamSequenceDictionary & SamReadGroupDi... tree | commitdiff
2011-10-11 derekCleanup in SortTool tree | commitdiff
2011-10-11 derekBug fix in BgzfStream I/O tree | commitdiff
2011-10-11 derekFixed typo tree | commitdiff
2011-10-11 derekCleanup missed by earlier "includes cleanup" commit tree | commitdiff
2011-10-11 derekRemoved index cache mode tree | commitdiff
2011-10-10 derekCleaned up intra-API includes & moved version numbers... tree | commitdiff
2011-10-10 derekUpdated Doxygen comments tree | commitdiff
2011-10-09 derekConverted intervals from 0-based, CLOSED to 0-based... tree | commitdiff
2011-10-07 derekCleaned up output/exception/asserts, etc after last... tree | commitdiff
2011-10-07 derekMerge with earlier IODevice work tree | commitdiff
2011-10-07 derekRemoved STDERR pollution by API tree | commitdiff
2011-10-04 derekFirst stab at templated tag access in BamAlignment tree | commitdiff
2011-10-04 derekRemoved duplicated method that snuck past a prior merge... tree | commitdiff
2011-10-03 derekmerge conflict tree | commitdiff
2011-10-03 derekMultiReader (&MultiMerger) now using Algorithms::Sort... tree | commitdiff
2011-09-30 derekInitial test run of new BamAlgorithms tree | commitdiff
2011-09-28 derekFix: unmapped reads now pushed to end of coordinate... tree | commitdiff
2011-09-27 derekFixed typo in error messages tree | commitdiff
2011-09-27 Derek BarnettMerge pull request #16 from gabeiscoding/patch-2 tree | commitdiff
2011-09-23 gabeiscodingIn standard indexed BAM files with with sparce coverage... tree | commitdiff
2011-09-10 derekMerge branches 'master' and 'iodevice' into iodevice tree | commitdiff
2011-09-10 derekMinor cleanup tree | commitdiff
2011-09-09 derekRemoved unnecessary peek-and-rewind behavior in BamMult... tree | commitdiff
2011-09-09 derekRemoved 'core mode' concept from BamMultiReader internals tree | commitdiff
2011-09-09 derekRefactored shared pipe/file behavior into ILocalIODevice tree | commitdiff
2011-09-09 derekMerge branches 'master' and 'iodevice' into iodevice tree | commitdiff
2011-09-09 derekBasic internal implementation of BamFile & BamPipe tree | commitdiff
2011-09-08 Derek BarnettMerge pull request #15 from gabeiscoding/patch-1 tree | commitdiff
2011-09-08 gabeiscodingBug discovered. The chunkStop was not being read from... tree | commitdiff
2011-09-07 derekAdded empty IBamIODevice.h tree | commitdiff
2011-09-02 derekAdded support for "-" as indicator for stdin/stdout tree | commitdiff
2011-09-02 derekAdded "isSingleton" property to filter tool tree | commitdiff
2011-07-27 derekImplemented binary search through bins in BAI tree | commitdiff
2011-07-06 derekAdded a -minMQ (minimum map quality) option to ResolveTool tree | commitdiff
2011-06-28 Derek BarnettMerge pull request #13 from alecchap/master tree | commitdiff
2011-06-28 derekAdded unique-alignment checks for ResolveTool tree | commitdiff
2011-06-28 Alec ChapmanFix Visual Studio compiler errors. tree | commitdiff
2011-06-23 derekFixed -fPIC issue for CentOS users. tree | commitdiff
2011-06-17 derekRemoved pessimistic warnings when jumping to regions... tree | commitdiff
2011-06-17 derekAdded re-calculation of BamAlignment's BinID during tree | commitdiff
2011-06-14 derekImplemented better coupling of unmapped reads with... tree | commitdiff
2011-06-14 derekFurther fixes for ISIZE-handling in ResolveTool tree | commitdiff
2011-06-13 derekFixed some signed/unsigned InsertSize bugs in ResolveTool tree | commitdiff
2011-06-11 derekConvertTool fix: removed extra space in (BAM->FASTA... tree | commitdiff
2011-06-11 derekCreated 3 modes for ResolveTool: makeStats, markPairs... tree | commitdiff
2011-06-11 derekCleaned up help formatting & added some string utilities tree | commitdiff
2011-06-07 derekAdded new ResolveTool - for paired-end resolution.... tree | commitdiff
2011-06-07 derekMinor cleanup to toolkit code formatting. tree | commitdiff
2011-05-10 derekFixed minimum offset error in BAI jumping tree | commitdiff
2011-05-05 Derek BarnettMerge pull request #9 from bookest/patch-1 tree | commitdiff
2011-05-05 Christopher Grim'make install' should install bin/bamtools tree | commitdiff
2011-04-27 derekRemoved debug statements that snuck into last commit tree | commitdiff
2011-04-27 derekFixed regression bug in index formats. Wasn't properly... tree | commitdiff
2011-04-22 derekAdditional attempt to force -fPIC on CentOS tree | commitdiff
2011-04-22 derekModified BamAlignment in attempt to resolve symbol... tree | commitdiff
2011-04-19 derekBrought API up to compliance with recent SAM Format... tree | commitdiff
2011-04-05 derekRolled back the BGZF buffer size to the original 64K... tree | commitdiff
2011-04-05 derekMajor performance boost to startup & random-access... tree | commitdiff
2011-03-23 derekMajor update to BamTools version 1.0 tree | commitdiff
2011-02-24 derekAttempt to fix SamHeaderVersion compile bug tree | commitdiff
2011-01-19 derekBug fix in SamHeaderVersion::SetVersion() tree | commitdiff
2011-01-19 derekMissed bug fix in BamMultiMerger in early commit. Fixed... tree | commitdiff
2011-01-17 derekAdded ExportHeader command for BamConstants.h tree | commitdiff
2011-01-17 derekRemoved SamHeaderValidatorPrivate pimpl. No real need... tree | commitdiff
2011-01-17 derekAdded UNSORTED to BamMultiReader::SortOrder types.... tree | commitdiff
2011-01-13 derekMinor formatting cleanup tree | commitdiff
2011-01-12 derekMinor update to API version 0.9.3 - addition of SamHead... tree | commitdiff
2011-01-12 derekAdded BamConstants.h tree | commitdiff
2011-01-12 derekRemoved explicit keyword from SamHeader-related object... tree | commitdiff
2011-01-12 derekUpdate to BamTools API 0.9.2 with exposure of SamHeader... tree | commitdiff
2011-01-12 derekAdded explicit copy ctors to SamHeader data structures tree | commitdiff
2010-12-24 derekAdded SAM header-handling classes for read/write/validate. tree | commitdiff
2010-12-24 derekUpdated to 0.9.1 tree | commitdiff
2010-12-24 derekImplemented proper -byname sorting (finally). tree | commitdiff
2010-12-24 derekAdded static library to build step. tree | commitdiff
2010-12-22 derekMoved BuildCharData() from BamReader to BamAlignment tree | commitdiff
2010-12-16 derekFixed: Improper sorting -byname tree | commitdiff
2010-12-15 derekAdded creation of include/ folder in bamtools root... tree | commitdiff
2010-12-13 derekMinor formatting cleanup tree | commitdiff
2010-12-13 derekMade BamAlignment flag queries symmetrical tree | commitdiff
2010-12-07 derekFixed: handling BamAlignments with limited char data tree | commitdiff
2010-12-06 derekFixed : improper exit code from FilterTool tree | commitdiff
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Branch of bamtools which has rudimentary Debian packaging