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2011-01-12	derek	Removed explicit keyword from SamHeader-related object...	commit \| commitdiff \| tree \| snapshot
2011-01-12	derek	Update to BamTools API 0.9.2 with exposure of SamHeader...	commit \| commitdiff \| tree \| snapshot
2011-01-12	derek	Added explicit copy ctors to SamHeader data structures	commit \| commitdiff \| tree \| snapshot
2010-12-24	derek	Added SAM header-handling classes for read/write/validate.	commit \| commitdiff \| tree \| snapshot
2010-12-24	derek	Updated to 0.9.1	commit \| commitdiff \| tree \| snapshot
2010-12-24	derek	Implemented proper -byname sorting (finally).	commit \| commitdiff \| tree \| snapshot
2010-12-24	derek	Added static library to build step.	commit \| commitdiff \| tree \| snapshot
2010-12-22	derek	Moved BuildCharData() from BamReader to BamAlignment	commit \| commitdiff \| tree \| snapshot
2010-12-16	derek	Fixed: Improper sorting -byname	commit \| commitdiff \| tree \| snapshot
2010-12-15	derek	Added creation of include/ folder in bamtools root...	commit \| commitdiff \| tree \| snapshot
2010-12-13	derek	Minor formatting cleanup	commit \| commitdiff \| tree \| snapshot
2010-12-13	derek	Made BamAlignment flag queries symmetrical	commit \| commitdiff \| tree \| snapshot
2010-12-07	derek	Fixed: handling BamAlignments with limited char data	commit \| commitdiff \| tree \| snapshot
2010-12-06	derek	Fixed : improper exit code from FilterTool	commit \| commitdiff \| tree \| snapshot
2010-12-06	derek	Fixed: core mode setting for BamMultiReader::Open(...	commit \| commitdiff \| tree \| snapshot
2010-12-06	derek	Added new RevertTool to the toolkit	commit \| commitdiff \| tree \| snapshot
2010-12-03	derek	Fixed: bug in the BamReader::Jump() codepath, specifica...	commit \| commitdiff \| tree \| snapshot
2010-11-22	derek	Moved private implementation API files to internal...	commit \| commitdiff \| tree \| snapshot
2010-11-22	derek	Added proper import of bamtools version info from CMake	commit \| commitdiff \| tree \| snapshot
2010-11-22	derek	Fixed BamRegion bug: previously only checked if refID...	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Continued breaking up of monolithic classes: extracted...	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Extracted BamReaderPrivate & BamWriterPrivate from...	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Added UTILS_EXPORT macro to classes in BamTools utility...	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Added API_EXPORT macro to classes in BamTools API	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Removed commented (library export) definitions from...	commit \| commitdiff \| tree \| snapshot
2010-11-19	derek	Migrated to CMake build system.	commit \| commitdiff \| tree \| snapshot
2010-11-18	derek	Changed GetNextAlignmentCore() calls to GetNextAlignmen...	commit \| commitdiff \| tree \| snapshot
2010-11-15	derek	Minor formatting cleanup	commit \| commitdiff \| tree \| snapshot
2010-10-27	derek	Removed more non-standard STL calls from BamIndex.cpp	commit \| commitdiff \| tree \| snapshot
2010-10-27	derek	Merge branch 'master' of git://github.com/ekg/bamtools	commit \| commitdiff \| tree \| snapshot
2010-10-27	derek	Removed non-standard stl::map method calls	commit \| commitdiff \| tree \| snapshot
2010-10-27	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-10-27	Erik Garrison	clarified no-index behavior in bam multi reader	commit \| commitdiff \| tree \| snapshot
2010-10-25	derek	Updated BamTools version information.	commit \| commitdiff \| tree \| snapshot
2010-10-24	derek	Updated README	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Merge branch 'master' of git://github.com/ekg/bamtools	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Updating README... still a work in progress	commit \| commitdiff \| tree \| snapshot
2010-10-21	Erik Garrison	add index caching mode setter to BamMultiReader	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Fixed NoIndexCaching behavior	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Merge branch 'master' of git://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Implemented index cache mode for both BAI & BTI formats	commit \| commitdiff \| tree \| snapshot
2010-10-21	Derek	Implemented index cache mode for both BAI & BTI formats	commit \| commitdiff \| tree \| snapshot
2010-10-16	Derek	modified/clarified some help & usage messages	commit \| commitdiff \| tree \| snapshot
2010-10-09	Derek	Changed BamAlignment::SupportData from private to public.	commit \| commitdiff \| tree \| snapshot
2010-10-09	Derek	Fixed: bug(s) related to empty references and regions.	commit \| commitdiff \| tree \| snapshot
2010-10-05	Derek	Minor formatting, commenting cleanup	commit \| commitdiff \| tree \| snapshot
2010-10-04	derek	Added tag support in filter tool.	commit \| commitdiff \| tree \| snapshot
2010-10-04	derek	Reviewed BAM to YAML conversion contribution (thank...	commit \| commitdiff \| tree \| snapshot
2010-09-29	Erik Garrison	convert: cleanup of prior fix, report if no index file...	commit \| commitdiff \| tree \| snapshot
2010-09-29	Erik Garrison	prior commit caused bug with convert	commit \| commitdiff \| tree \| snapshot
2010-09-28	Erik Garrison	exposes cigar string data to bamtools filter	commit \| commitdiff \| tree \| snapshot
2010-09-28	Erik Garrison	added reader.Open checks to a number of tools	commit \| commitdiff \| tree \| snapshot
2010-09-28	Chase Miller	Added Yaml for outputing BamAlignments.	commit \| commitdiff \| tree \| snapshot
2010-09-28	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-23	Derek	Fixed lack of reverse complemented output in BAM -...	commit \| commitdiff \| tree \| snapshot
2010-09-23	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-22	Derek	Implemented 'compound rule' logic in the FilterTool...	commit \| commitdiff \| tree \| snapshot
2010-09-20	Derek	Cleaned up SplitTool internal implementation. Use of...	commit \| commitdiff \| tree \| snapshot
2010-09-20	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-19	Derek	Removed a backup text file that snuck into an earlier...	commit \| commitdiff \| tree \| snapshot
2010-09-19	Derek	Added implementation of new SplitTool. This tool split...	commit \| commitdiff \| tree \| snapshot
2010-09-19	Derek	Added GetTagType() to BamAlignment	commit \| commitdiff \| tree \| snapshot
2010-09-18	Derek	Updated to match new BamAlignment.h includes	commit \| commitdiff \| tree \| snapshot
2010-09-18	Derek	Missed api/Makefile in last commit.	commit \| commitdiff \| tree \| snapshot
2010-09-18	Derek	Moved BamAlignment data structure out to its own .h...	commit \| commitdiff \| tree \| snapshot
2010-09-18	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-18	Derek	Fixed: bug related to accessing data (or regions with...	commit \| commitdiff \| tree \| snapshot
2010-09-17	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-16	Derek	On second thought, moved the (non-indexing) constants...	commit \| commitdiff \| tree \| snapshot
2010-09-16	Derek	Did some housekeeping in BamAux.h - moved some constant...	commit \| commitdiff \| tree \| snapshot
2010-09-16	Derek	Missed an update to BamToolsIndex code in a previous...	commit \| commitdiff \| tree \| snapshot
2010-09-16	Derek	Added new PileupEngine to the toolkit. This is used...	commit \| commitdiff \| tree \| snapshot
2010-09-15	Derek	Added option for users to specifiy half-open (1-based...	commit \| commitdiff \| tree \| snapshot
2010-09-13	Erik Garrison	Merge branch 'master' of http://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-13	Derek	Fixed off-by-one error in BamAlignment::GetEndPosition()	commit \| commitdiff \| tree \| snapshot
2010-09-11	Erik Garrison	updated debugging output in BamIndex, seek vs. calculat...	commit \| commitdiff \| tree \| snapshot
2010-09-11	Erik Garrison	Added more verbose debugging output to BamMultiReader...	commit \| commitdiff \| tree \| snapshot
2010-09-10	Derek	Reimplemented BamToolsIndex for bug fix and performance...	commit \| commitdiff \| tree \| snapshot
2010-09-10	Derek	Removed debug output statement that slipped into last...	commit \| commitdiff \| tree \| snapshot
2010-09-10	Derek	Reorganizing index/jumping calls. Now all BamReader...	commit \| commitdiff \| tree \| snapshot
2010-09-08	Erik Garrison	prefer bamtools index in BamMultiReader	commit \| commitdiff \| tree \| snapshot
2010-09-08	Erik Garrison	Merge branch 'master' of git://github.com/pezmaster31...	commit \| commitdiff \| tree \| snapshot
2010-09-07	Derek	Relicensed the source code used in bamtools_options...	commit \| commitdiff \| tree \| snapshot
2010-09-07	Derek	Documentation update	commit \| commitdiff \| tree \| snapshot
2010-09-07	Derek	Added -region option to bamtools_merge	commit \| commitdiff \| tree \| snapshot
2010-09-07	Derek	Previously missed a line in BamReader.cpp with the...	commit \| commitdiff \| tree \| snapshot
2010-09-03	Derek	Large-scale API indexing re-organization:	commit \| commitdiff \| tree \| snapshot
2010-09-03	Derek	Modified Utilities::FileExists() so it doesnt rely...	commit \| commitdiff \| tree \| snapshot
2010-09-03	Derek	Cleaned up index file handling throughout toolkit....	commit \| commitdiff \| tree \| snapshot
2010-09-03	Derek	Added IsIndexLoaded() public method to BamReader. Allow...	commit \| commitdiff \| tree \| snapshot
2010-09-02	Derek	Modified help description for -bti option	commit \| commitdiff \| tree \| snapshot
2010-09-01	Derek	Added uncompressed output as default behavior for Filte...	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Posted implementation of FilterTool.	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Minor formatting & commenting update	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Updated bamtools_utilities with #defines	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Updating bamtools_options	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Added bamtools_filter_engine.*	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Removed -pg debug flag from Makefile CXXFLAGS, accident...	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Forgot to add jsoncpp/json.h in a previous commit	commit \| commitdiff \| tree \| snapshot
2010-08-30	Derek	Fixed: Calls to GetEndPosition() rely on CIGAR data...	commit \| commitdiff \| tree \| snapshot
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