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bamtools.git
2010-10-21 Erik Garrisonadd index caching mode setter to BamMultiReader commit | commitdiff | tree | snapshot
2010-10-21 DerekFixed NoIndexCaching behavior commit | commitdiff | tree | snapshot
2010-10-21 DerekMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats commit | commitdiff | tree | snapshot
2010-10-21 DerekImplemented index cache mode for both BAI & BTI formats commit | commitdiff | tree | snapshot
2010-10-16 Derekmodified/clarified some help & usage messages commit | commitdiff | tree | snapshot
2010-10-09 DerekChanged BamAlignment::SupportData from private to public. commit | commitdiff | tree | snapshot
2010-10-09 DerekFixed: bug(s) related to empty references and regions. commit | commitdiff | tree | snapshot
2010-10-05 DerekMinor formatting, commenting cleanup commit | commitdiff | tree | snapshot
2010-10-04 derekAdded tag support in filter tool. commit | commitdiff | tree | snapshot
2010-10-04 derekReviewed BAM to YAML conversion contribution (thank... commit | commitdiff | tree | snapshot
2010-09-29 Erik Garrisonconvert: cleanup of prior fix, report if no index file... commit | commitdiff | tree | snapshot
2010-09-29 Erik Garrisonprior commit caused bug with convert commit | commitdiff | tree | snapshot
2010-09-28 Erik Garrisonexposes cigar string data to bamtools filter commit | commitdiff | tree | snapshot
2010-09-28 Erik Garrisonadded reader.Open checks to a number of tools commit | commitdiff | tree | snapshot
2010-09-28 Chase MillerAdded Yaml for outputing BamAlignments. commit | commitdiff | tree | snapshot
2010-09-28 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-23 DerekFixed lack of reverse complemented output in BAM -... commit | commitdiff | tree | snapshot
2010-09-23 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-22 DerekImplemented 'compound rule' logic in the FilterTool... commit | commitdiff | tree | snapshot
2010-09-20 DerekCleaned up SplitTool internal implementation. Use of... commit | commitdiff | tree | snapshot
2010-09-20 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-19 DerekRemoved a backup text file that snuck into an earlier... commit | commitdiff | tree | snapshot
2010-09-19 DerekAdded implementation of new SplitTool. This tool split... commit | commitdiff | tree | snapshot
2010-09-19 DerekAdded GetTagType() to BamAlignment commit | commitdiff | tree | snapshot
2010-09-18 DerekUpdated to match new BamAlignment.h includes commit | commitdiff | tree | snapshot
2010-09-18 DerekMissed api/Makefile in last commit. commit | commitdiff | tree | snapshot
2010-09-18 DerekMoved BamAlignment data structure out to its own .h... commit | commitdiff | tree | snapshot
2010-09-18 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-18 DerekFixed: bug related to accessing data (or regions with... commit | commitdiff | tree | snapshot
2010-09-17 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-16 DerekOn second thought, moved the (non-indexing) constants... commit | commitdiff | tree | snapshot
2010-09-16 DerekDid some housekeeping in BamAux.h - moved some constant... commit | commitdiff | tree | snapshot
2010-09-16 DerekMissed an update to BamToolsIndex code in a previous... commit | commitdiff | tree | snapshot
2010-09-16 DerekAdded new PileupEngine to the toolkit. This is used... commit | commitdiff | tree | snapshot
2010-09-15 DerekAdded option for users to specifiy half-open (1-based... commit | commitdiff | tree | snapshot
2010-09-13 Erik GarrisonMerge branch 'master' of http://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-13 DerekFixed off-by-one error in BamAlignment::GetEndPosition() commit | commitdiff | tree | snapshot
2010-09-11 Erik Garrisonupdated debugging output in BamIndex, seek vs. calculat... commit | commitdiff | tree | snapshot
2010-09-11 Erik GarrisonAdded more verbose debugging output to BamMultiReader... commit | commitdiff | tree | snapshot
2010-09-10 DerekReimplemented BamToolsIndex for bug fix and performance... commit | commitdiff | tree | snapshot
2010-09-10 DerekRemoved debug output statement that slipped into last... commit | commitdiff | tree | snapshot
2010-09-10 DerekReorganizing index/jumping calls. Now all BamReader... commit | commitdiff | tree | snapshot
2010-09-08 Erik Garrisonprefer bamtools index in BamMultiReader commit | commitdiff | tree | snapshot
2010-09-08 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-09-07 DerekRelicensed the source code used in bamtools_options... commit | commitdiff | tree | snapshot
2010-09-07 DerekDocumentation update commit | commitdiff | tree | snapshot
2010-09-07 DerekAdded -region option to bamtools_merge commit | commitdiff | tree | snapshot
2010-09-07 DerekPreviously missed a line in BamReader.cpp with the... commit | commitdiff | tree | snapshot
2010-09-03 DerekLarge-scale API indexing re-organization: commit | commitdiff | tree | snapshot
2010-09-03 DerekModified Utilities::FileExists() so it doesnt rely... commit | commitdiff | tree | snapshot
2010-09-03 DerekCleaned up index file handling throughout toolkit.... commit | commitdiff | tree | snapshot
2010-09-03 DerekAdded IsIndexLoaded() public method to BamReader. Allow... commit | commitdiff | tree | snapshot
2010-09-02 DerekModified help description for -bti option commit | commitdiff | tree | snapshot
2010-09-01 DerekAdded uncompressed output as default behavior for Filte... commit | commitdiff | tree | snapshot
2010-08-30 DerekPosted implementation of FilterTool. commit | commitdiff | tree | snapshot
2010-08-30 DerekMinor formatting & commenting update commit | commitdiff | tree | snapshot
2010-08-30 DerekUpdated bamtools_utilities with #defines commit | commitdiff | tree | snapshot
2010-08-30 DerekUpdating bamtools_options commit | commitdiff | tree | snapshot
2010-08-30 DerekAdded bamtools_filter_engine.* commit | commitdiff | tree | snapshot
2010-08-30 DerekRemoved -pg debug flag from Makefile CXXFLAGS, accident... commit | commitdiff | tree | snapshot
2010-08-30 DerekForgot to add jsoncpp/json.h in a previous commit commit | commitdiff | tree | snapshot
2010-08-30 DerekFixed: Calls to GetEndPosition() rely on CIGAR data... commit | commitdiff | tree | snapshot
2010-08-30 DerekAdded JsonCPP code to repo. Will be used by FilterTool... commit | commitdiff | tree | snapshot
2010-08-20 Erik Garrisonchange printf's to fprint(stderr, commit | commitdiff | tree | snapshot
2010-08-18 DerekMissed a Makefile in last commit - just adding header... commit | commitdiff | tree | snapshot
2010-08-18 DerekAdded simple header comments to all Makefiles, to help... commit | commitdiff | tree | snapshot
2010-08-18 DerekModified Makefile to ensure creation of bin/ and obj... commit | commitdiff | tree | snapshot
2010-08-18 DerekReorganized source tree & build system commit | commitdiff | tree | snapshot
2010-08-18 DerekMinor formatting cleanup in BamIndex.* commit | commitdiff | tree | snapshot
2010-08-17 DerekModified the way BGZF sets up uncompressed output.... commit | commitdiff | tree | snapshot
2010-08-17 DerekModified BamWriter::Open() to return bool on success... commit | commitdiff | tree | snapshot
2010-08-17 DerekAdded write-uncompressed flag to BGZF. Commit includes... commit | commitdiff | tree | snapshot
2010-08-06 DerekMerge git://github.com/ekg/bamtools commit | commitdiff | tree | snapshot
2010-08-06 DerekMinor formatting cleanup: really just an update to... commit | commitdiff | tree | snapshot
2010-08-05 Erik Garrisonfor json output in bamtools convert commit | commitdiff | tree | snapshot
2010-08-04 DerekBug fix in BamReader::Jump() commit | commitdiff | tree | snapshot
2010-07-27 DerekAdded AddTag/EditTag/RemoveTag methods to BamAlignment... commit | commitdiff | tree | snapshot
2010-07-23 DerekReworded bamtools stats general help description commit | commitdiff | tree | snapshot
2010-07-23 DerekMostly cosmetic fixes. A few tweaks to subtool options... commit | commitdiff | tree | snapshot
2010-07-23 DerekImplemented basic alignment stats (count/%) for most... commit | commitdiff | tree | snapshot
2010-07-22 DerekVarious cleanups. Added -noheader to SAM conversion... commit | commitdiff | tree | snapshot
2010-07-22 DerekForgot to update Makefile with last commit commit | commitdiff | tree | snapshot
2010-07-22 DerekRemoved SamTool (bamtools sam ...) from toolkit. This... commit | commitdiff | tree | snapshot
2010-07-22 DerekFixed variable length tag data retrieval in BamAlignmen... commit | commitdiff | tree | snapshot
2010-07-22 DerekFixed: remove unnecessary EOF write attempt for read... commit | commitdiff | tree | snapshot
2010-07-21 DerekForgot to include updated bamtools 'main' with RandomTo... commit | commitdiff | tree | snapshot
2010-07-21 DerekAdded the <cctype> include to BamAux to explicitly... commit | commitdiff | tree | snapshot
2010-07-20 DerekFixed fopen-related typo in bamtools_fasta.* commit | commitdiff | tree | snapshot
2010-07-20 DerekAdded basic implementation of RandomTool. This generate... commit | commitdiff | tree | snapshot
2010-07-20 DerekModified BamMultiReader::Open() to return bool. Still... commit | commitdiff | tree | snapshot
2010-07-19 DerekAdded cross-platform LFS for tell/seek. Removed fopen64... commit | commitdiff | tree | snapshot
2010-07-15 DerekFixed Rewind(). Now using LoadNextAlignment() instead... commit | commitdiff | tree | snapshot
2010-07-15 DerekModified Rewind() to check actual data present when... commit | commitdiff | tree | snapshot
2010-07-15 DerekModified handling of BamAlignmentSupportData. This... commit | commitdiff | tree | snapshot
2010-07-13 DerekPurely cosmetic udpate. Cleaned up some commented block... commit | commitdiff | tree | snapshot
2010-07-13 DerekUpdated Makefile for fasta & pileup commit | commitdiff | tree | snapshot
2010-07-13 DerekAdded support for reading FASTA sequences, as well... commit | commitdiff | tree | snapshot
2010-07-13 DerekBegun basic pileup conversion commit | commitdiff | tree | snapshot
2010-07-09 DerekAdded simple PrintBed() method; plan to add PrintWiggle... commit | commitdiff | tree | snapshot
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Branch of bamtools which has rudimentary Debian packaging