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2010-07-21	Derek	Forgot to include updated bamtools 'main' with RandomTo...	commit \| commitdiff \| tree \| snapshot
2010-07-21	Derek	Added the <cctype> include to BamAux to explicitly...	commit \| commitdiff \| tree \| snapshot
2010-07-20	Derek	Fixed fopen-related typo in bamtools_fasta.*	commit \| commitdiff \| tree \| snapshot
2010-07-20	Derek	Added basic implementation of RandomTool. This generate...	commit \| commitdiff \| tree \| snapshot
2010-07-20	Derek	Modified BamMultiReader::Open() to return bool. Still...	commit \| commitdiff \| tree \| snapshot
2010-07-19	Derek	Added cross-platform LFS for tell/seek. Removed fopen64...	commit \| commitdiff \| tree \| snapshot
2010-07-15	Derek	Fixed Rewind(). Now using LoadNextAlignment() instead...	commit \| commitdiff \| tree \| snapshot
2010-07-15	Derek	Modified Rewind() to check actual data present when...	commit \| commitdiff \| tree \| snapshot
2010-07-15	Derek	Modified handling of BamAlignmentSupportData. This...	commit \| commitdiff \| tree \| snapshot
2010-07-13	Derek	Purely cosmetic udpate. Cleaned up some commented block...	commit \| commitdiff \| tree \| snapshot
2010-07-13	Derek	Updated Makefile for fasta & pileup	commit \| commitdiff \| tree \| snapshot
2010-07-13	Derek	Added support for reading FASTA sequences, as well...	commit \| commitdiff \| tree \| snapshot
2010-07-13	Derek	Begun basic pileup conversion	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Added simple PrintBed() method; plan to add PrintWiggle...	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Fixed typos in last commit.	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Reorganized convert tool code. Restored stdin by defaul...	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Merge http://github.com/ekg/bamtools	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Fixed: proper handling of BamAlignment::AlignedBases...	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Updated index and count sub-tools to recognize new...	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Separated indexing ops to new class. Implemented a...	commit \| commitdiff \| tree \| snapshot
2010-07-09	Derek	Enforced proper handling of large files (>4Gb) on 32...	commit \| commitdiff \| tree \| snapshot
2010-07-07	Erik Garrison	Merge BamMultiReader and SetRegion into bamtools convert	commit \| commitdiff \| tree \| snapshot
2010-07-07	Erik Garrison	Remove heavy-handed failure mode in BamMultiReader...	commit \| commitdiff \| tree \| snapshot
2010-06-28	Derek	Removed accidental commit of .o files	commit \| commitdiff \| tree \| snapshot
2010-06-28	Derek	Modified BamReader(and BGZF)::Open() to return bool...	commit \| commitdiff \| tree \| snapshot
2010-06-22	Derek	Updated temp file path stubs to reflect input BAM file...	commit \| commitdiff \| tree \| snapshot
2010-06-22	Derek	Rough implementation of sort tool. Generate lots of...	commit \| commitdiff \| tree \| snapshot
2010-06-21	Erik Garrison	Gracefully handle empty files with the BamMultiReader	commit \| commitdiff \| tree \| snapshot
2010-06-18	Erik Garrison	integration of SetRegion into BamMultiReader	commit \| commitdiff \| tree \| snapshot
2010-06-18	Erik Garrison	moved bamtools_count to use BamRegion	commit \| commitdiff \| tree \| snapshot
2010-06-17	Derek	Modified Jump() scheme to take better account of specif...	commit \| commitdiff \| tree \| snapshot
2010-06-17	Derek	Modified BamReaderPrivate::GetOffset() & BinsFromRegion...	commit \| commitdiff \| tree \| snapshot
2010-06-17	Derek	Added concept of a fully specified region of interest...	commit \| commitdiff \| tree \| snapshot
2010-06-10	Erik Garrison	change merger to use GetNextAlignmentCore	commit \| commitdiff \| tree \| snapshot
2010-06-10	Erik Garrison	Merge branch 'master' of git://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-06-10	Derek	Moved BamAlignmentSupportData into BamAlignment data...	commit \| commitdiff \| tree \| snapshot
2010-06-09	Erik Garrison	further cleanup of duplicate @RG tag warning reporting	commit \| commitdiff \| tree \| snapshot
2010-06-09	Erik Garrison	added warning for duplicate @RG tag in header	commit \| commitdiff \| tree \| snapshot
2010-06-09	Erik Garrison	fixed potential bug with previous commit	commit \| commitdiff \| tree \| snapshot
2010-06-09	Erik Garrison	fixed bug with @RG handling	commit \| commitdiff \| tree \| snapshot
2010-06-09	Erik Garrison	Merge branch 'master' of git://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-06-09	Derek	Removed accidental add of object files	commit \| commitdiff \| tree \| snapshot
2010-06-09	Derek	Added GetNextAlignmentCore() to BamReader API as well...	commit \| commitdiff \| tree \| snapshot
2010-06-08	Erik Garrison	BamMultiReader data structure rewrite	commit \| commitdiff \| tree \| snapshot
2010-06-08	Erik Garrison	json output	commit \| commitdiff \| tree \| snapshot
2010-06-08	Derek	Fixed output of tag types c & C. Removed atoi() call...	commit \| commitdiff \| tree \| snapshot
2010-06-07	Derek	This fixes the out-of-range exception. Though there...	commit \| commitdiff \| tree \| snapshot
2010-06-07	Erik Garrison	pass ostream variable to print functions in convert	commit \| commitdiff \| tree \| snapshot
2010-06-07	Derek	Began rolling over bamtools_sam into bamtools_convert...	commit \| commitdiff \| tree \| snapshot
2010-06-07	Derek	Fixed typo in settings config.	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Added ConvertTool.h/cpp. Not yet implemented.	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Updated README	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Added FilterTool.h/cpp. Not yet implemented.	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Added a second Utilities::ParseRegionString() that...	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Cleaned up CountTool, by extending Utilities::ParseRegi...	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Minor formatting/commenting fixes. No major changes...	commit \| commitdiff \| tree \| snapshot
2010-06-03	Derek	Implemented bamtools sam. Required new unpack methods...	commit \| commitdiff \| tree \| snapshot
2010-06-02	Derek	Removed a debug output statement that piggybacked into...	commit \| commitdiff \| tree \| snapshot
2010-06-02	Derek	Implemented CountTool, cleaned up MergeTool.	commit \| commitdiff \| tree \| snapshot
2010-06-02	Derek	Put utilities into own class with static methods	commit \| commitdiff \| tree \| snapshot
2010-06-02	Derek	Implemented Mosaik-style command line parser, instead...	commit \| commitdiff \| tree \| snapshot
2010-05-27	Derek	Mostly cleaned up help & usage messages. Added MIT...	commit \| commitdiff \| tree \| snapshot
2010-05-26	Derek	Removed BamTrimMain.cpp. Missed that one in last commit...	commit \| commitdiff \| tree \| snapshot
2010-05-26	Derek	Removed BamConversionMain.cpp and BamDumpMain.cpp....	commit \| commitdiff \| tree \| snapshot
2010-05-26	Derek	Removed bamtools_test from Makefile. Was a temporary...	commit \| commitdiff \| tree \| snapshot
2010-05-26	Derek	Reorganization of toolkit. Split subtools out to own...	commit \| commitdiff \| tree \| snapshot
2010-05-25	Derek	Added templated GetTag() method, compile tested, but...	commit \| commitdiff \| tree \| snapshot
2010-05-21	Erik Garrison	Complete prior commit	commit \| commitdiff \| tree \| snapshot
2010-05-21	Erik Garrison	bamtools executable	commit \| commitdiff \| tree \| snapshot
2010-05-07	barnett	Removed Boost dependency in BamMultiReader.cpp	commit \| commitdiff \| tree \| snapshot
2010-05-07	barnett	Didnt actually add BamMultiMerge and BamMultiReader...	commit \| commitdiff \| tree \| snapshot
2010-05-06	barnett	Added BamMultiReader and BamMultiMerge	commit \| commitdiff \| tree \| snapshot
2010-04-14	barnett	Moved BamReaderPrivate::CalculateAlignmentEnd() to...	commit \| commitdiff \| tree \| snapshot
2010-04-06	barnett	Major speedup of BamReader - removed full character...	commit \| commitdiff \| tree \| snapshot
2010-03-31	barnett	Updated BamAux modified date	commit \| commitdiff \| tree \| snapshot
2010-03-31	barnett	Restored BamDumpMain to old version without dumping...	commit \| commitdiff \| tree \| snapshot
2010-03-31	barnett	Major fix in handling tag data in BamAux.h... checking...	commit \| commitdiff \| tree \| snapshot
2010-03-31	barnett	Major dumb fix in BamAux.h BamAlignment::SkipToNextTag...	commit \| commitdiff \| tree \| snapshot
2010-03-31	barnett	Modified BamDump to spit out TagData (for debugging)	commit \| commitdiff \| tree \| snapshot
2010-03-30	barnett	Updated contact info in README	commit \| commitdiff \| tree \| snapshot
2010-03-30	barnett	Had some typos in last commit. Fixed.	commit \| commitdiff \| tree \| snapshot
2010-03-30	barnett	Fixed: off by 1 in BamWriter, variable tag parsing...	commit \| commitdiff \| tree \| snapshot
2010-01-11	barnett	Added #include<cstdio> to BamAux.h to cover use of...	commit \| commitdiff \| tree \| snapshot
2010-01-11	barnett	Fixed fread() related compiler warnings. Fixed std...	commit \| commitdiff \| tree \| snapshot
2010-01-08	barnett	Updated BamAux	commit \| commitdiff \| tree \| snapshot
2010-01-08	barnett	Added empty block EOF to BGZF::Close	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Fixed README typos	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Updated README	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Fixed a few more signed/unsigned issues	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Fixed some signed/unsigned int issues	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Updated Makefile	commit \| commitdiff \| tree \| snapshot
2009-12-08	barnett	Major overhaul to BamTools	commit \| commitdiff \| tree \| snapshot
2009-10-01	barnett	Fix of signed/unsigned in BamReader methods	commit \| commitdiff \| tree \| snapshot
2009-10-01	barnett	Modified BamAlignment data members to match BAM specs...	commit \| commitdiff \| tree \| snapshot
2009-09-30	barnett	changed SIZEOF_INT to BT_SIZEOF_INT - namespace collisi...	commit \| commitdiff \| tree \| snapshot
2009-09-25	barnett	Changed BamAlignment::InsertSize to signed int... need...	commit \| commitdiff \| tree \| snapshot
2009-09-17	barnett	Changed BGZF data member to pointer... to force buffer...	commit \| commitdiff \| tree \| snapshot
2009-08-04	mikaels	fixed a bug where the terminal null wasn't being saved...	commit \| commitdiff \| tree \| snapshot
2009-07-16	barnett	Changed BAM_CORE_SIZE to unsigned int to remove signed...	commit \| commitdiff \| tree \| snapshot
2009-07-16	barnett	Added BamConversion back to BamTools	commit \| commitdiff \| tree \| snapshot
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