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bamtools.git
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
2010-08-18 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
2010-07-09 DerekFixed typos in last commit. commit | commitdiff | tree | snapshot
2010-07-09 DerekReorganized convert tool code. Restored stdin by defaul... commit | commitdiff | tree | snapshot
2010-07-09 DerekMerge http://github.com/ekg/bamtools commit | commitdiff | tree | snapshot
2010-07-09 DerekFixed: proper handling of BamAlignment::AlignedBases... commit | commitdiff | tree | snapshot
2010-07-09 DerekUpdated index and count sub-tools to recognize new... commit | commitdiff | tree | snapshot
2010-07-09 DerekSeparated indexing ops to new class. Implemented a... commit | commitdiff | tree | snapshot
2010-07-09 DerekEnforced proper handling of large files (>4Gb) on 32... commit | commitdiff | tree | snapshot
2010-07-07 Erik GarrisonMerge BamMultiReader and SetRegion into bamtools convert commit | commitdiff | tree | snapshot
2010-07-07 Erik GarrisonRemove heavy-handed failure mode in BamMultiReader... commit | commitdiff | tree | snapshot
2010-06-28 DerekRemoved accidental commit of .o files commit | commitdiff | tree | snapshot
2010-06-28 DerekModified BamReader(and BGZF)::Open() to return bool... commit | commitdiff | tree | snapshot
2010-06-22 DerekUpdated temp file path stubs to reflect input BAM file... commit | commitdiff | tree | snapshot
2010-06-22 DerekRough implementation of sort tool. Generate lots of... commit | commitdiff | tree | snapshot
2010-06-21 Erik GarrisonGracefully handle empty files with the BamMultiReader commit | commitdiff | tree | snapshot
2010-06-18 Erik Garrisonintegration of SetRegion into BamMultiReader commit | commitdiff | tree | snapshot
2010-06-18 Erik Garrisonmoved bamtools_count to use BamRegion commit | commitdiff | tree | snapshot
2010-06-17 DerekModified Jump() scheme to take better account of specif... commit | commitdiff | tree | snapshot
2010-06-17 DerekModified BamReaderPrivate::GetOffset() & BinsFromRegion... commit | commitdiff | tree | snapshot
2010-06-17 DerekAdded concept of a fully specified region of interest... commit | commitdiff | tree | snapshot
2010-06-10 Erik Garrisonchange merger to use GetNextAlignmentCore commit | commitdiff | tree | snapshot
2010-06-10 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-06-10 DerekMoved BamAlignmentSupportData into BamAlignment data... commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfurther cleanup of duplicate @RG tag warning reporting commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonadded warning for duplicate @RG tag in header commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfixed potential bug with previous commit commit | commitdiff | tree | snapshot
2010-06-09 Erik Garrisonfixed bug with @RG handling commit | commitdiff | tree | snapshot
2010-06-09 Erik GarrisonMerge branch 'master' of git://github.com/pezmaster31... commit | commitdiff | tree | snapshot
2010-06-09 DerekRemoved accidental add of object files commit | commitdiff | tree | snapshot
2010-06-09 DerekAdded GetNextAlignmentCore() to BamReader API as well... commit | commitdiff | tree | snapshot
2010-06-08 Erik GarrisonBamMultiReader data structure rewrite commit | commitdiff | tree | snapshot
2010-06-08 Erik Garrisonjson output commit | commitdiff | tree | snapshot
2010-06-08 DerekFixed output of tag types c & C. Removed atoi() call... commit | commitdiff | tree | snapshot
2010-06-07 DerekThis fixes the out-of-range exception. Though there... commit | commitdiff | tree | snapshot
2010-06-07 Erik Garrisonpass ostream variable to print functions in convert commit | commitdiff | tree | snapshot
2010-06-07 DerekBegan rolling over bamtools_sam into bamtools_convert... commit | commitdiff | tree | snapshot
2010-06-07 DerekFixed typo in settings config. commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded ConvertTool.h/cpp. Not yet implemented. commit | commitdiff | tree | snapshot
2010-06-03 DerekUpdated README commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded FilterTool.h/cpp. Not yet implemented. commit | commitdiff | tree | snapshot
2010-06-03 DerekAdded a second Utilities::ParseRegionString() that... commit | commitdiff | tree | snapshot
2010-06-03 DerekCleaned up CountTool, by extending Utilities::ParseRegi... commit | commitdiff | tree | snapshot
2010-06-03 DerekMinor formatting/commenting fixes. No major changes... commit | commitdiff | tree | snapshot
2010-06-03 DerekImplemented bamtools sam. Required new unpack methods... commit | commitdiff | tree | snapshot
2010-06-02 DerekRemoved a debug output statement that piggybacked into... commit | commitdiff | tree | snapshot
2010-06-02 DerekImplemented CountTool, cleaned up MergeTool. commit | commitdiff | tree | snapshot
2010-06-02 DerekPut utilities into own class with static methods commit | commitdiff | tree | snapshot
2010-06-02 DerekImplemented Mosaik-style command line parser, instead... commit | commitdiff | tree | snapshot
2010-05-27 DerekMostly cleaned up help & usage messages. Added MIT... commit | commitdiff | tree | snapshot
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Branch of bamtools which has rudimentary Debian packaging