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bamtools.git
2010-09-07
Derek
Added -region option to bamtools_merge
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2010-09-07
Derek
Previously missed a line in BamReader.cpp with the...
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2010-09-03
Derek
Large-scale API indexing re-organization:
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2010-09-03
Derek
Modified Utilities::FileExists() so it doesnt rely...
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2010-09-03
Derek
Cleaned up index file handling throughout toolkit....
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2010-09-03
Derek
Added IsIndexLoaded() public method to BamReader. Allow...
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2010-09-02
Derek
Modified help description for -bti option
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2010-09-01
Derek
Added uncompressed output as default behavior for Filte...
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2010-08-30
Derek
Posted implementation of FilterTool.
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2010-08-30
Derek
Minor formatting & commenting update
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2010-08-30
Derek
Updated bamtools_utilities with #defines
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2010-08-30
Derek
Updating bamtools_options
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2010-08-30
Derek
Added bamtools_filter_engine.*
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2010-08-30
Derek
Removed -pg debug flag from Makefile CXXFLAGS, accident...
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2010-08-30
Derek
Forgot to add jsoncpp/json.h in a previous commit
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2010-08-30
Derek
Fixed: Calls to GetEndPosition() rely on CIGAR data...
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2010-08-30
Derek
Added JsonCPP code to repo. Will be used by FilterTool...
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2010-08-18
Derek
Missed a Makefile in last commit - just adding header...
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2010-08-18
Derek
Added simple header comments to all Makefiles, to help...
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2010-08-18
Derek
Modified Makefile to ensure creation of bin/ and obj...
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2010-08-18
Derek
Reorganized source tree & build system
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2010-08-18
Derek
Minor formatting cleanup in BamIndex.*
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2010-08-17
Derek
Modified the way BGZF sets up uncompressed output....
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2010-08-17
Derek
Modified BamWriter::Open() to return bool on success...
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2010-08-17
Derek
Added write-uncompressed flag to BGZF. Commit includes...
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2010-08-06
Derek
Merge git://github.com/ekg/bamtools
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2010-08-06
Derek
Minor formatting cleanup: really just an update to...
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2010-08-05
Erik Garrison
for json output in bamtools convert
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2010-08-04
Derek
Bug fix in BamReader::Jump()
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2010-07-27
Derek
Added AddTag/EditTag/RemoveTag methods to BamAlignment...
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2010-07-23
Derek
Reworded bamtools stats general help description
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2010-07-23
Derek
Mostly cosmetic fixes. A few tweaks to subtool options...
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2010-07-23
Derek
Implemented basic alignment stats (count/%) for most...
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2010-07-22
Derek
Various cleanups. Added -noheader to SAM conversion...
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2010-07-22
Derek
Forgot to update Makefile with last commit
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2010-07-22
Derek
Removed SamTool (bamtools sam ...) from toolkit. This...
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2010-07-22
Derek
Fixed variable length tag data retrieval in BamAlignmen...
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2010-07-22
Derek
Fixed: remove unnecessary EOF write attempt for read...
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2010-07-21
Derek
Forgot to include updated bamtools 'main' with RandomTo...
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2010-07-21
Derek
Added the <cctype> include to BamAux to explicitly...
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2010-07-20
Derek
Fixed fopen-related typo in bamtools_fasta.*
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2010-07-20
Derek
Added basic implementation of RandomTool. This generate...
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2010-07-20
Derek
Modified BamMultiReader::Open() to return bool. Still...
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2010-07-19
Derek
Added cross-platform LFS for tell/seek. Removed fopen64...
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2010-07-15
Derek
Fixed Rewind(). Now using LoadNextAlignment() instead...
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2010-07-15
Derek
Modified Rewind() to check actual data present when...
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2010-07-15
Derek
Modified handling of BamAlignmentSupportData. This...
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2010-07-13
Derek
Purely cosmetic udpate. Cleaned up some commented block...
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2010-07-13
Derek
Updated Makefile for fasta & pileup
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2010-07-13
Derek
Added support for reading FASTA sequences, as well...
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2010-07-13
Derek
Begun basic pileup conversion
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2010-07-09
Derek
Added simple PrintBed() method; plan to add PrintWiggle...
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2010-07-09
Derek
Fixed typos in last commit.
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2010-07-09
Derek
Reorganized convert tool code. Restored stdin by defaul...
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2010-07-09
Derek
Merge http://github.com/ekg/bamtools
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2010-07-09
Derek
Fixed: proper handling of BamAlignment::AlignedBases...
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2010-07-09
Derek
Updated index and count sub-tools to recognize new...
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2010-07-09
Derek
Separated indexing ops to new class. Implemented a...
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2010-07-09
Derek
Enforced proper handling of large files (>4Gb) on 32...
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2010-07-07
Erik Garrison
Merge BamMultiReader and SetRegion into bamtools convert
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2010-07-07
Erik Garrison
Remove heavy-handed failure mode in BamMultiReader...
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2010-06-28
Derek
Removed accidental commit of .o files
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2010-06-28
Derek
Modified BamReader(and BGZF)::Open() to return bool...
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2010-06-22
Derek
Updated temp file path stubs to reflect input BAM file...
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2010-06-22
Derek
Rough implementation of sort tool. Generate lots of...
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2010-06-21
Erik Garrison
Gracefully handle empty files with the BamMultiReader
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2010-06-18
Erik Garrison
integration of SetRegion into BamMultiReader
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2010-06-18
Erik Garrison
moved bamtools_count to use BamRegion
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2010-06-17
Derek
Modified Jump() scheme to take better account of specif...
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2010-06-17
Derek
Modified BamReaderPrivate::GetOffset() & BinsFromRegion...
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2010-06-17
Derek
Added concept of a fully specified region of interest...
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2010-06-10
Erik Garrison
change merger to use GetNextAlignmentCore
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2010-06-10
Erik Garrison
Merge branch 'master' of git://github.com/pezmaster31...
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2010-06-10
Derek
Moved BamAlignmentSupportData into BamAlignment data...
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2010-06-09
Erik Garrison
further cleanup of duplicate @RG tag warning reporting
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2010-06-09
Erik Garrison
added warning for duplicate @RG tag in header
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2010-06-09
Erik Garrison
fixed potential bug with previous commit
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2010-06-09
Erik Garrison
fixed bug with @RG handling
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2010-06-09
Erik Garrison
Merge branch 'master' of git://github.com/pezmaster31...
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2010-06-09
Derek
Removed accidental add of object files
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2010-06-09
Derek
Added GetNextAlignmentCore() to BamReader API as well...
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2010-06-08
Erik Garrison
BamMultiReader data structure rewrite
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2010-06-08
Erik Garrison
json output
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2010-06-08
Derek
Fixed output of tag types c & C. Removed atoi() call...
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2010-06-07
Derek
This fixes the out-of-range exception. Though there...
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2010-06-07
Erik Garrison
pass ostream variable to print functions in convert
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2010-06-07
Derek
Began rolling over bamtools_sam into bamtools_convert...
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2010-06-07
Derek
Fixed typo in settings config.
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2010-06-03
Derek
Added ConvertTool.h/cpp. Not yet implemented.
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2010-06-03
Derek
Updated README
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2010-06-03
Derek
Added FilterTool.h/cpp. Not yet implemented.
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2010-06-03
Derek
Added a second Utilities::ParseRegionString() that...
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2010-06-03
Derek
Cleaned up CountTool, by extending Utilities::ParseRegi...
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2010-06-03
Derek
Minor formatting/commenting fixes. No major changes...
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2010-06-03
Derek
Implemented bamtools sam. Required new unpack methods...
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2010-06-02
Derek
Removed a debug output statement that piggybacked into...
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2010-06-02
Derek
Implemented CountTool, cleaned up MergeTool.
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2010-06-02
Derek
Put utilities into own class with static methods
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2010-06-02
Derek
Implemented Mosaik-style command line parser, instead...
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2010-05-27
Derek
Mostly cleaned up help & usage messages. Added MIT...
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