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bamtools.git
2010-07-09 DerekFixed: proper handling of BamAlignment::AlignedBases... commit | commitdiff | tree | snapshot
2010-07-09 DerekUpdated index and count sub-tools to recognize new... commit | commitdiff | tree | snapshot
2010-07-09 DerekSeparated indexing ops to new class. Implemented a... commit | commitdiff | tree | snapshot
2010-07-09 DerekEnforced proper handling of large files (>4Gb) on 32... commit | commitdiff | tree | snapshot
2010-06-28 DerekRemoved accidental commit of .o files commit | commitdiff | tree | snapshot
2010-06-28 DerekModified BamReader(and BGZF)::Open() to return bool... commit | commitdiff | tree | snapshot
2010-06-22 DerekUpdated temp file path stubs to reflect input BAM file... commit | commitdiff | tree | snapshot
2010-06-22 DerekRough implementation of sort tool. Generate lots of... commit | commitdiff | tree | snapshot
2010-06-21 Erik GarrisonGracefully handle empty files with the BamMultiReader commit | commitdiff | tree | snapshot
2010-06-18 Erik Garrisonintegration of SetRegion into BamMultiReader commit | commitdiff | tree | snapshot
2010-06-18 Erik Garrisonmoved bamtools_count to use BamRegion commit | commitdiff | tree | snapshot
2010-06-17 DerekModified Jump() scheme to take better account of specif... commit | commitdiff | tree | snapshot
2010-06-17 DerekModified BamReaderPrivate::GetOffset() & BinsFromRegion... commit | commitdiff | tree | snapshot
2010-06-17 DerekAdded concept of a fully specified region of interest... commit | commitdiff | tree | snapshot
2010-06-10 Erik Garrisonchange merger to use GetNextAlignmentCore commit | commitdiff | tree | snapshot
2010-06-10 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-06-10 DerekMoved BamAlignmentSupportData into BamAlignment data... commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfurther cleanup of duplicate @RG tag warning reporting commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonadded warning for duplicate @RG tag in header commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfixed potential bug with previous commit commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfixed bug with @RG handling commit | commitdiff | tree | snapshot
2010-06-09 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-06-09 DerekRemoved accidental add of object files commit | commitdiff | tree | snapshot
2010-06-09 DerekAdded GetNextAlignmentCore() to BamReader API as well... commit | commitdiff | tree | snapshot
2010-06-08 Erik GarrisonBamMultiReader data structure rewrite commit | commitdiff | tree | snapshot
2010-06-08 Erik Garrisonjson output commit | commitdiff | tree | snapshot
2010-06-08 DerekFixed output of tag types c & C. Removed atoi() call... commit | commitdiff | tree | snapshot
2010-06-07 DerekThis fixes the out-of-range exception. Though there... commit | commitdiff | tree | snapshot
2010-06-07 Erik Garrisonpass ostream variable to print functions in convert commit | commitdiff | tree | snapshot
2010-06-07 DerekBegan rolling over bamtools_sam into bamtools_convert... commit | commitdiff | tree | snapshot
2010-06-07 DerekFixed typo in settings config. commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded ConvertTool.h/cpp. Not yet implemented. commit | commitdiff | tree | snapshot
2010-06-03 DerekUpdated README commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded FilterTool.h/cpp. Not yet implemented. commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded a second Utilities::ParseRegionString() that... commit | commitdiff | tree | snapshot
2010-06-03 DerekCleaned up CountTool, by extending Utilities::ParseRegi... commit | commitdiff | tree | snapshot
2010-06-03 DerekMinor formatting/commenting fixes. No major changes... commit | commitdiff | tree | snapshot
2010-06-03 DerekImplemented bamtools sam. Required new unpack methods... commit | commitdiff | tree | snapshot
2010-06-02 DerekRemoved a debug output statement that piggybacked into... commit | commitdiff | tree | snapshot
2010-06-02 DerekImplemented CountTool, cleaned up MergeTool. commit | commitdiff | tree | snapshot
2010-06-02 DerekPut utilities into own class with static methods commit | commitdiff | tree | snapshot
2010-06-02 DerekImplemented Mosaik-style command line parser, instead... commit | commitdiff | tree | snapshot
2010-05-27 DerekMostly cleaned up help & usage messages. Added MIT... commit | commitdiff | tree | snapshot
2010-05-26 DerekRemoved BamTrimMain.cpp. Missed that one in last commit... commit | commitdiff | tree | snapshot
2010-05-26 DerekRemoved BamConversionMain.cpp and BamDumpMain.cpp.... commit | commitdiff | tree | snapshot
2010-05-26 DerekRemoved bamtools_test from Makefile. Was a temporary... commit | commitdiff | tree | snapshot
2010-05-26 DerekReorganization of toolkit. Split subtools out to own... commit | commitdiff | tree | snapshot
2010-05-25 DerekAdded templated GetTag() method, compile tested, but... commit | commitdiff | tree | snapshot
2010-05-21 Erik GarrisonComplete prior commit commit | commitdiff | tree | snapshot
2010-05-21 Erik Garrisonbamtools executable commit | commitdiff | tree | snapshot
2010-05-07 barnettRemoved Boost dependency in BamMultiReader.cpp commit | commitdiff | tree | snapshot
2010-05-07 barnettDidnt actually add BamMultiMerge and BamMultiReader... commit | commitdiff | tree | snapshot
2010-05-06 barnettAdded BamMultiReader and BamMultiMerge commit | commitdiff | tree | snapshot
2010-04-14 barnettMoved BamReaderPrivate::CalculateAlignmentEnd() to... commit | commitdiff | tree | snapshot
2010-04-06 barnettMajor speedup of BamReader - removed full character... commit | commitdiff | tree | snapshot
2010-03-31 barnettUpdated BamAux modified date commit | commitdiff | tree | snapshot
2010-03-31 barnettRestored BamDumpMain to old version without dumping... commit | commitdiff | tree | snapshot
2010-03-31 barnettMajor fix in handling tag data in BamAux.h... checking... commit | commitdiff | tree | snapshot
2010-03-31 barnettMajor dumb fix in BamAux.h BamAlignment::SkipToNextTag... commit | commitdiff | tree | snapshot
2010-03-31 barnettModified BamDump to spit out TagData (for debugging) commit | commitdiff | tree | snapshot
2010-03-30 barnettUpdated contact info in README commit | commitdiff | tree | snapshot
2010-03-30 barnettHad some typos in last commit. Fixed. commit | commitdiff | tree | snapshot
2010-03-30 barnettFixed: off by 1 in BamWriter, variable tag parsing... commit | commitdiff | tree | snapshot
2010-01-11 barnettAdded #include<cstdio> to BamAux.h to cover use of... commit | commitdiff | tree | snapshot
2010-01-11 barnettFixed fread() related compiler warnings. Fixed std... commit | commitdiff | tree | snapshot
2010-01-08 barnettUpdated BamAux commit | commitdiff | tree | snapshot
2010-01-08 barnettAdded empty block EOF to BGZF::Close commit | commitdiff | tree | snapshot
2009-12-08 barnettFixed README typos commit | commitdiff | tree | snapshot
2009-12-08 barnettUpdated README commit | commitdiff | tree | snapshot
2009-12-08 barnettFixed a few more signed/unsigned issues commit | commitdiff | tree | snapshot
2009-12-08 barnettFixed some signed/unsigned int issues commit | commitdiff | tree | snapshot
2009-12-08 barnettUpdated Makefile commit | commitdiff | tree | snapshot
2009-12-08 barnettMajor overhaul to BamTools commit | commitdiff | tree | snapshot
2009-10-01 barnettFix of signed/unsigned in BamReader methods commit | commitdiff | tree | snapshot
2009-10-01 barnettModified BamAlignment data members to match BAM specs... commit | commitdiff | tree | snapshot
2009-09-30 barnettchanged SIZEOF_INT to BT_SIZEOF_INT - namespace collisi... commit | commitdiff | tree | snapshot
2009-09-25 barnettChanged BamAlignment::InsertSize to signed int... need... commit | commitdiff | tree | snapshot
2009-09-17 barnettChanged BGZF data member to pointer... to force buffer... commit | commitdiff | tree | snapshot
2009-08-04 mikaelsfixed a bug where the terminal null wasn't being saved... commit | commitdiff | tree | snapshot
2009-07-16 barnettChanged BAM_CORE_SIZE to unsigned int to remove signed... commit | commitdiff | tree | snapshot
2009-07-16 barnettAdded BamConversion back to BamTools commit | commitdiff | tree | snapshot
2009-07-15 barnettUpdated README commit | commitdiff | tree | snapshot
2009-07-15 barnettFull update to SVN after combining BamReader and BamWri... commit | commitdiff | tree | snapshot
2009-05-18 barnettMajor overhaul of BamReader. No longer relying on bgzf... commit | commitdiff | tree | snapshot
2009-04-23 barnettHad signs reversed in GetOffset error check. Fixed commit | commitdiff | tree | snapshot
2009-04-23 barnettRemoved assertion in GetOffset(), now returns -1 if... commit | commitdiff | tree | snapshot
2009-04-19 barnettBug fix in BamMerge.cpp by Chip commit | commitdiff | tree | snapshot
2009-04-13 barnettChip - removed limits commit | commitdiff | tree | snapshot
2009-04-13 barnettAdded Chip's BamMerge to the repository commit | commitdiff | tree | snapshot
2009-04-11 mikaelsFixed some of the output for tag data. commit | commitdiff | tree | snapshot
2009-04-11 mikaelsForgot some include statements. commit | commitdiff | tree | snapshot
2009-04-11 mikaelsAdded tag data support. commit | commitdiff | tree | snapshot
2009-04-11 mikaelsAdded support for the tag data and provided a GetReadGr... commit | commitdiff | tree | snapshot
2009-04-11 mikaelsremoved DOS line endings commit | commitdiff | tree | snapshot
2009-04-10 mikaelsRemoved the profiling options since they shouldn't... commit | commitdiff | tree | snapshot
2009-04-10 mikaelsMade many improvements to the code that pass the strict... commit | commitdiff | tree | snapshot
2009-04-10 mikaelsUpdated the header text to give credit to the Broad... commit | commitdiff | tree | snapshot
2009-04-10 mikaelsDefined some of the non-standard data types for compati... commit | commitdiff | tree | snapshot
2009-04-10 mikaelsAdded BamConversion to the make clean command commit | commitdiff | tree | snapshot
2009-04-10 barnettUpdated BamReaderMain.cpp to remove unused variable... commit | commitdiff | tree | snapshot
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Branch of bamtools which has rudimentary Debian packaging