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2010-06-09	Derek	Removed accidental add of object files	commit \| commitdiff \| tree
2010-06-09	Derek	Added GetNextAlignmentCore() to BamReader API as well...	commit \| commitdiff \| tree
2010-06-08	Derek	Fixed output of tag types c & C. Removed atoi() call...	commit \| commitdiff \| tree
2010-06-07	Derek	This fixes the out-of-range exception. Though there...	commit \| commitdiff \| tree
2010-06-07	Derek	Began rolling over bamtools_sam into bamtools_convert...	commit \| commitdiff \| tree
2010-06-07	Derek	Fixed typo in settings config.	commit \| commitdiff \| tree
2010-06-03	Derek	Added ConvertTool.h/cpp. Not yet implemented.	commit \| commitdiff \| tree
2010-06-03	Derek	Updated README	commit \| commitdiff \| tree
2010-06-03	Derek	Added FilterTool.h/cpp. Not yet implemented.	commit \| commitdiff \| tree
2010-06-03	Derek	Added a second Utilities::ParseRegionString() that...	commit \| commitdiff \| tree
2010-06-03	Derek	Cleaned up CountTool, by extending Utilities::ParseRegionStr...	commit \| commitdiff \| tree
2010-06-03	Derek	Minor formatting/commenting fixes. No major changes...	commit \| commitdiff \| tree
2010-06-03	Derek	Implemented bamtools sam. Required new unpack methods...	commit \| commitdiff \| tree
2010-06-02	Derek	Removed a debug output statement that piggybacked into...	commit \| commitdiff \| tree
2010-06-02	Derek	Implemented CountTool, cleaned up MergeTool.	commit \| commitdiff \| tree
2010-06-02	Derek	Put utilities into own class with static methods	commit \| commitdiff \| tree
2010-06-02	Derek	Implemented Mosaik-style command line parser, instead...	commit \| commitdiff \| tree
2010-05-27	Derek	Mostly cleaned up help & usage messages. Added MIT...	commit \| commitdiff \| tree
2010-05-26	Derek	Removed BamTrimMain.cpp. Missed that one in last commit...	commit \| commitdiff \| tree
2010-05-26	Derek	Removed BamConversionMain.cpp and BamDumpMain.cpp....	commit \| commitdiff \| tree
2010-05-26	Derek	Removed bamtools_test from Makefile. Was a temporary...	commit \| commitdiff \| tree
2010-05-26	Derek	Reorganization of toolkit. Split subtools out to own...	commit \| commitdiff \| tree
2010-05-25	Derek	Added templated GetTag() method, compile tested, but...	commit \| commitdiff \| tree
2010-05-07	barnett	Removed Boost dependency in BamMultiReader.cpp	commit \| commitdiff \| tree
2010-05-07	barnett	Didnt actually add BamMultiMerge and BamMultiReader...	commit \| commitdiff \| tree
2010-05-06	barnett	Added BamMultiReader and BamMultiMerge	commit \| commitdiff \| tree
2010-04-14	barnett	Moved BamReaderPrivate::CalculateAlignmentEnd() to...	commit \| commitdiff \| tree
2010-04-06	barnett	Major speedup of BamReader - removed full character...	commit \| commitdiff \| tree
2010-03-31	barnett	Updated BamAux modified date	commit \| commitdiff \| tree
2010-03-31	barnett	Restored BamDumpMain to old version without dumping...	commit \| commitdiff \| tree
2010-03-31	barnett	Major fix in handling tag data in BamAux.h... checking...	commit \| commitdiff \| tree
2010-03-31	barnett	Major dumb fix in BamAux.h BamAlignment::SkipToNextTag...	commit \| commitdiff \| tree
2010-03-31	barnett	Modified BamDump to spit out TagData (for debugging)	commit \| commitdiff \| tree
2010-03-30	barnett	Updated contact info in README	commit \| commitdiff \| tree
2010-03-30	barnett	Had some typos in last commit. Fixed.	commit \| commitdiff \| tree
2010-03-30	barnett	Fixed: off by 1 in BamWriter, variable tag parsing...	commit \| commitdiff \| tree
2010-01-11	barnett	Added #include<cstdio> to BamAux.h to cover use of...	commit \| commitdiff \| tree
2010-01-11	barnett	Fixed fread() related compiler warnings. Fixed std...	commit \| commitdiff \| tree
2010-01-08	barnett	Updated BamAux	commit \| commitdiff \| tree
2010-01-08	barnett	Added empty block EOF to BGZF::Close	commit \| commitdiff \| tree
2009-12-08	barnett	Fixed README typos	commit \| commitdiff \| tree
2009-12-08	barnett	Updated README	commit \| commitdiff \| tree
2009-12-08	barnett	Fixed a few more signed/unsigned issues	commit \| commitdiff \| tree
2009-12-08	barnett	Fixed some signed/unsigned int issues	commit \| commitdiff \| tree
2009-12-08	barnett	Updated Makefile	commit \| commitdiff \| tree
2009-12-08	barnett	Major overhaul to BamTools	commit \| commitdiff \| tree
2009-10-01	barnett	Fix of signed/unsigned in BamReader methods	commit \| commitdiff \| tree
2009-10-01	barnett	Modified BamAlignment data members to match BAM specs...	commit \| commitdiff \| tree
2009-09-30	barnett	changed SIZEOF_INT to BT_SIZEOF_INT - namespace collision...	commit \| commitdiff \| tree
2009-09-25	barnett	Changed BamAlignment::InsertSize to signed int... need...	commit \| commitdiff \| tree
2009-09-17	barnett	Changed BGZF data member to pointer... to force buffer...	commit \| commitdiff \| tree
2009-07-16	barnett	Changed BAM_CORE_SIZE to unsigned int to remove signed...	commit \| commitdiff \| tree
2009-07-16	barnett	Added BamConversion back to BamTools	commit \| commitdiff \| tree
2009-07-15	barnett	Updated README	commit \| commitdiff \| tree
2009-07-15	barnett	Full update to SVN after combining BamReader and BamWriter...	commit \| commitdiff \| tree
2009-05-18	barnett	Major overhaul of BamReader. No longer relying on bgzf...	commit \| commitdiff \| tree
2009-04-23	barnett	Had signs reversed in GetOffset error check. Fixed	commit \| commitdiff \| tree
2009-04-23	barnett	Removed assertion in GetOffset(), now returns -1 if...	commit \| commitdiff \| tree
2009-04-19	barnett	Bug fix in BamMerge.cpp by Chip	commit \| commitdiff \| tree
2009-04-13	barnett	Chip - removed limits	commit \| commitdiff \| tree
2009-04-13	barnett	Added Chip's BamMerge to the repository	commit \| commitdiff \| tree
2009-04-10	barnett	Updated BamReaderMain.cpp to remove unused variable...	commit \| commitdiff \| tree
2009-04-10	barnett	creating directories	commit \| commitdiff \| tree

Branch of bamtools which has rudimentary Debian packaging

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