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