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