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2010-12-06	derek	Fixed: core mode setting for BamMultiReader::Open(...	commit \| commitdiff \| tree
2010-12-06	derek	Added new RevertTool to the toolkit	commit \| commitdiff \| tree
2010-12-03	derek	Fixed: bug in the BamReader::Jump() codepath, specifically the	commit \| commitdiff \| tree
2010-11-22	derek	Moved private implementation API files to internal...	commit \| commitdiff \| tree
2010-11-22	derek	Added proper import of bamtools version info from CMake	commit \| commitdiff \| tree
2010-11-22	derek	Fixed BamRegion bug: previously only checked if refID...	commit \| commitdiff \| tree
2010-11-19	derek	Continued breaking up of monolithic classes: extracted...	commit \| commitdiff \| tree
2010-11-19	derek	Extracted BamReaderPrivate & BamWriterPrivate from...	commit \| commitdiff \| tree
2010-11-19	derek	Added UTILS_EXPORT macro to classes in BamTools utility...	commit \| commitdiff \| tree
2010-11-19	derek	Added API_EXPORT macro to classes in BamTools API	commit \| commitdiff \| tree
2010-11-19	derek	Removed commented (library export) definitions from...	commit \| commitdiff \| tree
2010-11-19	derek	Migrated to CMake build system.	commit \| commitdiff \| tree
2010-11-18	derek	Changed GetNextAlignmentCore() calls to GetNextAlignment...	commit \| commitdiff \| tree
2010-11-15	derek	Minor formatting cleanup	commit \| commitdiff \| tree
2010-10-27	derek	Removed more non-standard STL calls from BamIndex.cpp	commit \| commitdiff \| tree
2010-10-27	derek	Merge branch 'master' of git://github.com/ekg/bamtools	commit \| commitdiff \| tree
2010-10-27	derek	Removed non-standard stl::map method calls	commit \| commitdiff \| tree
2010-10-25	derek	Updated BamTools version information.	commit \| commitdiff \| tree
2010-10-24	derek	Updated README	commit \| commitdiff \| tree
2010-10-21	Derek	Merge branch 'master' of git://github.com/ekg/bamtools	commit \| commitdiff \| tree
2010-10-21	Derek	Updating README... still a work in progress	commit \| commitdiff \| tree
2010-10-21	Derek	Fixed NoIndexCaching behavior	commit \| commitdiff \| tree
2010-10-21	Derek	Merge branch 'master' of git://github.com/pezmaster31...	commit \| commitdiff \| tree
2010-10-21	Derek	Implemented index cache mode for both BAI & BTI formats	commit \| commitdiff \| tree
2010-10-21	Derek	Implemented index cache mode for both BAI & BTI formats	commit \| commitdiff \| tree
2010-10-16	Derek	modified/clarified some help & usage messages	commit \| commitdiff \| tree
2010-10-09	Derek	Changed BamAlignment::SupportData from private to public.	commit \| commitdiff \| tree
2010-10-09	Derek	Fixed: bug(s) related to empty references and regions.	commit \| commitdiff \| tree
2010-10-05	Derek	Minor formatting, commenting cleanup	commit \| commitdiff \| tree
2010-09-23	Derek	Fixed lack of reverse complemented output in BAM -...	commit \| commitdiff \| tree
2010-09-22	Derek	Implemented 'compound rule' logic in the FilterTool...	commit \| commitdiff \| tree
2010-09-20	Derek	Cleaned up SplitTool internal implementation. Use of...	commit \| commitdiff \| tree
2010-09-19	Derek	Removed a backup text file that snuck into an earlier...	commit \| commitdiff \| tree
2010-09-19	Derek	Added implementation of new SplitTool. This tool splits...	commit \| commitdiff \| tree
2010-09-19	Derek	Added GetTagType() to BamAlignment	commit \| commitdiff \| tree
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
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