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2010-09-18	Derek	Updated to match new BamAlignment.h includes	commit \| commitdiff \| tree
2010-09-18	Derek	Missed api/Makefile in last commit.	commit \| commitdiff \| tree
2010-09-18	Derek	Moved BamAlignment data structure out to its own .h...	commit \| commitdiff \| tree
2010-09-18	Derek	Fixed: bug related to accessing data (or regions with...	commit \| commitdiff \| tree
2010-09-16	Derek	On second thought, moved the (non-indexing) constants...	commit \| commitdiff \| tree
2010-09-16	Derek	Did some housekeeping in BamAux.h - moved some constants...	commit \| commitdiff \| tree
2010-09-16	Derek	Missed an update to BamToolsIndex code in a previous...	commit \| commitdiff \| tree
2010-09-16	Derek	Added new PileupEngine to the toolkit. This is used...	commit \| commitdiff \| tree
2010-09-15	Derek	Added option for users to specifiy half-open (1-based...	commit \| commitdiff \| tree
2010-09-13	Derek	Fixed off-by-one error in BamAlignment::GetEndPosition()	commit \| commitdiff \| tree
2010-09-10	Derek	Reimplemented BamToolsIndex for bug fix and performance...	commit \| commitdiff \| tree
2010-09-10	Derek	Removed debug output statement that slipped into last...	commit \| commitdiff \| tree
2010-09-10	Derek	Reorganizing index/jumping calls. Now all BamReader...	commit \| commitdiff \| tree
2010-09-07	Derek	Relicensed the source code used in bamtools_options...	commit \| commitdiff \| tree
2010-09-07	Derek	Documentation update	commit \| commitdiff \| tree
2010-09-07	Derek	Added -region option to bamtools_merge	commit \| commitdiff \| tree
2010-09-07	Derek	Previously missed a line in BamReader.cpp with the...	commit \| commitdiff \| tree
2010-09-03	Derek	Large-scale API indexing re-organization:	commit \| commitdiff \| tree
2010-09-03	Derek	Modified Utilities::FileExists() so it doesnt rely...	commit \| commitdiff \| tree
2010-09-03	Derek	Cleaned up index file handling throughout toolkit....	commit \| commitdiff \| tree
2010-09-03	Derek	Added IsIndexLoaded() public method to BamReader. Allows...	commit \| commitdiff \| tree
2010-09-02	Derek	Modified help description for -bti option	commit \| commitdiff \| tree
2010-09-01	Derek	Added uncompressed output as default behavior for Filter...	commit \| commitdiff \| tree
2010-08-30	Derek	Posted implementation of FilterTool.	commit \| commitdiff \| tree
2010-08-30	Derek	Minor formatting & commenting update	commit \| commitdiff \| tree
2010-08-30	Derek	Updated bamtools_utilities with #defines	commit \| commitdiff \| tree
2010-08-30	Derek	Updating bamtools_options	commit \| commitdiff \| tree
2010-08-30	Derek	Added bamtools_filter_engine.*	commit \| commitdiff \| tree
2010-08-30	Derek	Removed -pg debug flag from Makefile CXXFLAGS, accidentally...	commit \| commitdiff \| tree
2010-08-30	Derek	Forgot to add jsoncpp/json.h in a previous commit	commit \| commitdiff \| tree
2010-08-30	Derek	Fixed: Calls to GetEndPosition() rely on CIGAR data...	commit \| commitdiff \| tree
2010-08-30	Derek	Added JsonCPP code to repo. Will be used by FilterTool...	commit \| commitdiff \| tree
2010-08-18	Derek	Missed a Makefile in last commit - just adding header...	commit \| commitdiff \| tree
2010-08-18	Derek	Added simple header comments to all Makefiles, to help...	commit \| commitdiff \| tree
2010-08-18	Derek	Modified Makefile to ensure creation of bin/ and obj...	commit \| commitdiff \| tree
2010-08-18	Derek	Reorganized source tree & build system	commit \| commitdiff \| tree
2010-08-18	Derek	Minor formatting cleanup in BamIndex.*	commit \| commitdiff \| tree
2010-08-17	Derek	Modified the way BGZF sets up uncompressed output....	commit \| commitdiff \| tree
2010-08-17	Derek	Modified BamWriter::Open() to return bool on success...	commit \| commitdiff \| tree
2010-08-17	Derek	Added write-uncompressed flag to BGZF. Commit includes...	commit \| commitdiff \| tree
2010-08-06	Derek	Merge git://github.com/ekg/bamtools	commit \| commitdiff \| tree
2010-08-06	Derek	Minor formatting cleanup: really just an update to...	commit \| commitdiff \| tree
2010-08-04	Derek	Bug fix in BamReader::Jump()	commit \| commitdiff \| tree
2010-07-27	Derek	Added AddTag/EditTag/RemoveTag methods to BamAlignment...	commit \| commitdiff \| tree
2010-07-23	Derek	Reworded bamtools stats general help description	commit \| commitdiff \| tree
2010-07-23	Derek	Mostly cosmetic fixes. A few tweaks to subtool options...	commit \| commitdiff \| tree
2010-07-23	Derek	Implemented basic alignment stats (count/%) for most...	commit \| commitdiff \| tree
2010-07-22	Derek	Various cleanups. Added -noheader to SAM conversion...	commit \| commitdiff \| tree
2010-07-22	Derek	Forgot to update Makefile with last commit	commit \| commitdiff \| tree
2010-07-22	Derek	Removed SamTool (bamtools sam ...) from toolkit. This...	commit \| commitdiff \| tree
2010-07-22	Derek	Fixed variable length tag data retrieval in BamAlignment...	commit \| commitdiff \| tree
2010-07-22	Derek	Fixed: remove unnecessary EOF write attempt for read...	commit \| commitdiff \| tree
2010-07-21	Derek	Forgot to include updated bamtools 'main' with RandomTool...	commit \| commitdiff \| tree
2010-07-21	Derek	Added the <cctype> include to BamAux to explicitly...	commit \| commitdiff \| tree
2010-07-20	Derek	Fixed fopen-related typo in bamtools_fasta.*	commit \| commitdiff \| tree
2010-07-20	Derek	Added basic implementation of RandomTool. This generates...	commit \| commitdiff \| tree
2010-07-20	Derek	Modified BamMultiReader::Open() to return bool. Still...	commit \| commitdiff \| tree
2010-07-19	Derek	Added cross-platform LFS for tell/seek. Removed fopen64...	commit \| commitdiff \| tree
2010-07-15	Derek	Fixed Rewind(). Now using LoadNextAlignment() instead...	commit \| commitdiff \| tree
2010-07-15	Derek	Modified Rewind() to check actual data present when...	commit \| commitdiff \| tree
2010-07-15	Derek	Modified handling of BamAlignmentSupportData. This...	commit \| commitdiff \| tree
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
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