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2010-07-13	Derek	Purely cosmetic udpate. Cleaned up some commented blocks...	commit \| commitdiff \| tree
2010-07-13	Derek	Updated Makefile for fasta & pileup	commit \| commitdiff \| tree
2010-07-13	Derek	Added support for reading FASTA sequences, as well...	commit \| commitdiff \| tree
2010-07-13	Derek	Begun basic pileup conversion	commit \| commitdiff \| tree
2010-07-09	Derek	Added simple PrintBed() method; plan to add PrintWiggle...	commit \| commitdiff \| tree
2010-07-09	Derek	Fixed typos in last commit.	commit \| commitdiff \| tree
2010-07-09	Derek	Reorganized convert tool code. Restored stdin by default...	commit \| commitdiff \| tree
2010-07-09	Derek	Merge http://github.com/ekg/bamtools	commit \| commitdiff \| tree
2010-07-09	Derek	Fixed: proper handling of BamAlignment::AlignedBases...	commit \| commitdiff \| tree
2010-07-09	Derek	Updated index and count sub-tools to recognize new...	commit \| commitdiff \| tree
2010-07-09	Derek	Separated indexing ops to new class. Implemented a...	commit \| commitdiff \| tree
2010-07-09	Derek	Enforced proper handling of large files (>4Gb) on 32...	commit \| commitdiff \| tree
2010-06-28	Derek	Removed accidental commit of .o files	commit \| commitdiff \| tree
2010-06-28	Derek	Modified BamReader(and BGZF)::Open() to return bool...	commit \| commitdiff \| tree
2010-06-22	Derek	Updated temp file path stubs to reflect input BAM file...	commit \| commitdiff \| tree
2010-06-22	Derek	Rough implementation of sort tool. Generate lots of...	commit \| commitdiff \| tree
2010-06-17	Derek	Modified Jump() scheme to take better account of specified...	commit \| commitdiff \| tree
2010-06-17	Derek	Modified BamReaderPrivate::GetOffset() & BinsFromRegion...	commit \| commitdiff \| tree
2010-06-17	Derek	Added concept of a fully specified region of interest...	commit \| commitdiff \| tree
2010-06-10	Derek	Moved BamAlignmentSupportData into BamAlignment data...	commit \| commitdiff \| tree
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

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