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2010-12-06 derekFixed: core mode setting for BamMultiReader::Open(... tree | commitdiff
2010-12-06 derekAdded new RevertTool to the toolkit tree | commitdiff
2010-12-03 derekFixed: bug in the BamReader::Jump() codepath, specifica... tree | commitdiff
2010-11-22 derekMoved private implementation API files to internal... tree | commitdiff
2010-11-22 derekAdded proper import of bamtools version info from CMake tree | commitdiff
2010-11-22 derekFixed BamRegion bug: previously only checked if refID... tree | commitdiff
2010-11-19 derekContinued breaking up of monolithic classes: extracted... tree | commitdiff
2010-11-19 derekExtracted BamReaderPrivate & BamWriterPrivate from... tree | commitdiff
2010-11-19 derekAdded UTILS_EXPORT macro to classes in BamTools utility... tree | commitdiff
2010-11-19 derekAdded API_EXPORT macro to classes in BamTools API tree | commitdiff
2010-11-19 derekRemoved commented (library export) definitions from... tree | commitdiff
2010-11-19 derekMigrated to CMake build system. tree | commitdiff
2010-11-18 derekChanged GetNextAlignmentCore() calls to GetNextAlignmen... tree | commitdiff
2010-11-15 derekMinor formatting cleanup tree | commitdiff
2010-10-27 derekRemoved more non-standard STL calls from BamIndex.cpp tree | commitdiff
2010-10-27 derekMerge branch 'master' of git://github.com/ekg/bamtools tree | commitdiff
2010-10-27 derekRemoved non-standard stl::map method calls tree | commitdiff
2010-10-27 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-10-27 Erik Garrisonclarified no-index behavior in bam multi reader tree | commitdiff
2010-10-25 derekUpdated BamTools version information. tree | commitdiff
2010-10-21 DerekMerge branch 'master' of git://github.com/ekg/bamtools tree | commitdiff
2010-10-21 Erik Garrisonadd index caching mode setter to BamMultiReader tree | commitdiff
2010-10-21 DerekFixed NoIndexCaching behavior tree | commitdiff
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats tree | commitdiff
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats tree | commitdiff
2010-10-16 Derekmodified/clarified some help & usage messages tree | commitdiff
2010-10-09 DerekChanged BamAlignment::SupportData from private to public. tree | commitdiff
2010-10-09 DerekFixed: bug(s) related to empty references and regions. tree | commitdiff
2010-10-05 DerekMinor formatting, commenting cleanup tree | commitdiff
2010-10-04 derekAdded tag support in filter tool. tree | commitdiff
2010-10-04 derekReviewed BAM to YAML conversion contribution (thank... tree | commitdiff
2010-09-29 Erik Garrisonconvert: cleanup of prior fix, report if no index file... tree | commitdiff
2010-09-29 Erik Garrisonprior commit caused bug with convert tree | commitdiff
2010-09-28 Erik Garrisonexposes cigar string data to bamtools filter tree | commitdiff
2010-09-28 Erik Garrisonadded reader.Open checks to a number of tools tree | commitdiff
2010-09-28 Chase MillerAdded Yaml for outputing BamAlignments. tree | commitdiff
2010-09-28 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-23 DerekFixed lack of reverse complemented output in BAM -... tree | commitdiff
2010-09-23 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-22 DerekImplemented 'compound rule' logic in the FilterTool... tree | commitdiff
2010-09-20 DerekCleaned up SplitTool internal implementation. Use of... tree | commitdiff
2010-09-20 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-19 DerekRemoved a backup text file that snuck into an earlier... tree | commitdiff
2010-09-19 DerekAdded implementation of new SplitTool. This tool split... tree | commitdiff
2010-09-19 DerekAdded GetTagType() to BamAlignment tree | commitdiff
2010-09-18 DerekUpdated to match new BamAlignment.h includes tree | commitdiff
2010-09-18 DerekMissed api/Makefile in last commit. tree | commitdiff
2010-09-18 DerekMoved BamAlignment data structure out to its own .h... tree | commitdiff
2010-09-18 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-18 DerekFixed: bug related to accessing data (or regions with... tree | commitdiff
2010-09-17 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-16 DerekOn second thought, moved the (non-indexing) constants... tree | commitdiff
2010-09-16 DerekDid some housekeeping in BamAux.h - moved some constant... tree | commitdiff
2010-09-16 DerekMissed an update to BamToolsIndex code in a previous... tree | commitdiff
2010-09-16 DerekAdded new PileupEngine to the toolkit. This is used... tree | commitdiff
2010-09-15 DerekAdded option for users to specifiy half-open (1-based... tree | commitdiff
2010-09-13 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... tree | commitdiff
2010-09-13 DerekFixed off-by-one error in BamAlignment::GetEndPosition() tree | commitdiff
2010-09-11 Erik Garrisonupdated debugging output in BamIndex, seek vs. calculat... tree | commitdiff
2010-09-11 Erik GarrisonAdded more verbose debugging output to BamMultiReader... tree | commitdiff
2010-09-10 DerekReimplemented BamToolsIndex for bug fix and performance... tree | commitdiff
2010-09-10 DerekRemoved debug output statement that slipped into last... tree | commitdiff
2010-09-10 DerekReorganizing index/jumping calls. Now all BamReader... tree | commitdiff
2010-09-08 Erik Garrisonprefer bamtools index in BamMultiReader tree | commitdiff
2010-09-08 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... tree | commitdiff
2010-09-07 DerekRelicensed the source code used in bamtools_options... tree | commitdiff
2010-09-07 DerekDocumentation update tree | commitdiff
2010-09-07 DerekAdded -region option to bamtools_merge tree | commitdiff
2010-09-07 DerekPreviously missed a line in BamReader.cpp with the... tree | commitdiff
2010-09-03 DerekLarge-scale API indexing re-organization: tree | commitdiff
2010-09-03 DerekModified Utilities::FileExists() so it doesnt rely... tree | commitdiff
2010-09-03 DerekCleaned up index file handling throughout toolkit.... tree | commitdiff
2010-09-03 DerekAdded IsIndexLoaded() public method to BamReader. Allow... tree | commitdiff
2010-09-02 DerekModified help description for -bti option tree | commitdiff
2010-09-01 DerekAdded uncompressed output as default behavior for Filte... tree | commitdiff
2010-08-30 DerekPosted implementation of FilterTool. tree | commitdiff
2010-08-30 DerekMinor formatting & commenting update tree | commitdiff
2010-08-30 DerekUpdated bamtools_utilities with #defines tree | commitdiff
2010-08-30 DerekUpdating bamtools_options tree | commitdiff
2010-08-30 DerekAdded bamtools_filter_engine.* tree | commitdiff
2010-08-30 DerekForgot to add jsoncpp/json.h in a previous commit tree | commitdiff
2010-08-30 DerekFixed: Calls to GetEndPosition() rely on CIGAR data... tree | commitdiff
2010-08-30 DerekAdded JsonCPP code to repo. Will be used by FilterTool... tree | commitdiff
2010-08-20 Erik Garrisonchange printf's to fprint(stderr, tree | commitdiff
2010-08-18 DerekMissed a Makefile in last commit - just adding header... tree | commitdiff
2010-08-18 DerekAdded simple header comments to all Makefiles, to help... tree | commitdiff
2010-08-18 DerekReorganized source tree & build system tree | commitdiff
Branch of bamtools which has rudimentary Debian packaging