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2012-04-04	derek	Added proper handling for empty or ignored ("*") alignment...	commit \| commitdiff \| tree
2012-04-04	derek	Fixed: invalidated by-name sort order in some cases	commit \| commitdiff \| tree
2012-03-27	derek	Fixed: sorting order lost during merge step of sort...	commit \| commitdiff \| tree
2012-03-26	Derek Barnett	Merge pull request #40 from tobiasmarschall/master	commit \| commitdiff \| tree
2012-03-26	Derek Barnett	Merge pull request #39 from leecbaker/master	commit \| commitdiff \| tree
2012-03-09	derek	FASTA reader - performance improvement for single-base...	commit \| commitdiff \| tree
2012-03-09	derek	PileupEngine performance improvement for high coverage	commit \| commitdiff \| tree
2012-03-09	derek	PileupEngine bugfix	commit \| commitdiff \| tree
2012-02-23	derek	Provided initialization values for previously unspecified...	commit \| commitdiff \| tree
2012-02-13	derek	Fixed: error in BamWriter metadata output on big-endian...	commit \| commitdiff \| tree
2012-01-17	derek	Fixed regression: missing EOF empty block on BgzfStream...	commit \| commitdiff \| tree
2012-01-14	derek	Fixed: const-related typo in last commit	commit \| commitdiff \| tree
2012-01-13	derek	Removed use of std::map::at() in HttpHeader, not a...	commit \| commitdiff \| tree
2012-01-05	derek	Fixed: bad_alloc in socket buffer on some machines	commit \| commitdiff \| tree
2011-12-08	derek	Nonstandard, user-defined tags now allowed in SAM header...	commit \| commitdiff \| tree
2011-12-08	derek	Added support for custom reference prefix in split...	commit \| commitdiff \| tree
2011-12-08	derek	Fixed: split tool crash when trying to split unmapped...	commit \| commitdiff \| tree
2011-12-08	derek	Fixed: premature EOF issues & updated Windows implementation	commit \| commitdiff \| tree
2011-12-08	derek	Rolled back test suite code from master until it's...	commit \| commitdiff \| tree
2011-12-08	derek	Fixed EOF issues on *nix platforms	commit \| commitdiff \| tree
2011-11-29	derek	Reorganized test suite source tree	commit \| commitdiff \| tree
2011-11-29	derek	Post-merge cleanup	commit \| commitdiff \| tree
2011-11-28	derek	merge with remoteio branch	commit \| commitdiff \| tree
2011-11-28	derek	Updated CMakeLists.txt files	commit \| commitdiff \| tree
2011-11-28	derek	Initial test suite commit	commit \| commitdiff \| tree
2011-11-17	derek	Basic Windows implementation	commit \| commitdiff \| tree
2011-11-15	derek	Removed spurious assert	commit \| commitdiff \| tree
2011-11-10	derek	Updated file headers (filename, license, description...	commit \| commitdiff \| tree
2011-11-10	derek	Added generic I/O device to BamIndex side of things	commit \| commitdiff \| tree
2011-11-09	derek	Added FTP support (text-tested, not BAM)	commit \| commitdiff \| tree
2011-11-07	derek	Implemented basic TCP support layer	commit \| commitdiff \| tree
2011-10-25	derek	Organized api/internal into subdirs	commit \| commitdiff \| tree
2011-10-17	derek	Removed some debugging 'error string' messages that...	commit \| commitdiff \| tree
2011-10-17	derek	Regression fixed: error in BamAlignment tag access...	commit \| commitdiff \| tree
2011-10-16	derek	Removed data duplication in last update to Sam*Dictionaries	commit \| commitdiff \| tree
2011-10-14	derek	Fixed regression: improper @SQ line ordering in SamHeader...	commit \| commitdiff \| tree
2011-10-14	derek	Regression fixed: wasn't properly merging from multiple...	commit \| commitdiff \| tree
2011-10-14	derek	Minor cleanup in FilterTool	commit \| commitdiff \| tree
2011-10-13	derek	Added GetSoftClips() method to BamAlignment	commit \| commitdiff \| tree
2011-10-12	derek	Major speedup in SamSequenceDictionary & SamReadGroupDiction...	commit \| commitdiff \| tree
2011-10-11	derek	Cleanup in SortTool	commit \| commitdiff \| tree
2011-10-11	derek	Bug fix in BgzfStream I/O	commit \| commitdiff \| tree
2011-10-11	derek	Fixed typo	commit \| commitdiff \| tree
2011-10-11	derek	Cleanup missed by earlier "includes cleanup" commit	commit \| commitdiff \| tree
2011-10-11	derek	Updated Doxyfile to reflect version 2.0.0	commit \| commitdiff \| tree
2011-10-11	derek	Removed index cache mode	commit \| commitdiff \| tree
2011-10-10	derek	Cleaned up intra-API includes & moved version numbers...	commit \| commitdiff \| tree
2011-10-10	derek	Updated Doxygen comments	commit \| commitdiff \| tree
2011-10-09	derek	Converted intervals from 0-based, CLOSED to 0-based...	commit \| commitdiff \| tree
2011-10-07	derek	Cleaned up output/exception/asserts, etc after last...	commit \| commitdiff \| tree
2011-10-07	derek	Merge with earlier IODevice work	commit \| commitdiff \| tree
2011-10-07	derek	Removed STDERR pollution by API	commit \| commitdiff \| tree
2011-10-04	derek	First stab at templated tag access in BamAlignment	commit \| commitdiff \| tree
2011-10-04	derek	Removed duplicated method that snuck past a prior merge...	commit \| commitdiff \| tree
2011-10-03	derek	merge conflict	commit \| commitdiff \| tree
2011-10-03	derek	MultiReader (&MultiMerger) now using Algorithms::Sort...	commit \| commitdiff \| tree
2011-09-30	derek	Initial test run of new BamAlgorithms	commit \| commitdiff \| tree
2011-09-28	derek	Fix: unmapped reads now pushed to end of coordinate...	commit \| commitdiff \| tree
2011-09-27	derek	Fixed typo in error messages	commit \| commitdiff \| tree
2011-09-27	Derek Barnett	Merge pull request #16 from gabeiscoding/patch-2	commit \| commitdiff \| tree
2011-09-10	derek	Merge branches 'master' and 'iodevice' into iodevice	commit \| commitdiff \| tree
2011-09-10	derek	Minor cleanup	commit \| commitdiff \| tree
2011-09-09	derek	Removed unnecessary peek-and-rewind behavior in BamMultiReader	commit \| commitdiff \| tree
2011-09-09	derek	Removed 'core mode' concept from BamMultiReader internals	commit \| commitdiff \| tree
2011-09-09	derek	Refactored shared pipe/file behavior into ILocalIODevice	commit \| commitdiff \| tree
2011-09-09	derek	Merge branches 'master' and 'iodevice' into iodevice	commit \| commitdiff \| tree
2011-09-09	derek	Basic internal implementation of BamFile & BamPipe	commit \| commitdiff \| tree
2011-09-08	Derek Barnett	Merge pull request #15 from gabeiscoding/patch-1	commit \| commitdiff \| tree
2011-09-07	derek	Added empty IBamIODevice.h	commit \| commitdiff \| tree
2011-09-02	derek	Added support for "-" as indicator for stdin/stdout	commit \| commitdiff \| tree
2011-09-02	derek	Added "isSingleton" property to filter tool	commit \| commitdiff \| tree
2011-07-27	derek	Implemented binary search through bins in BAI	commit \| commitdiff \| tree
2011-07-06	derek	Added a -minMQ (minimum map quality) option to ResolveTool	commit \| commitdiff \| tree
2011-06-28	Derek Barnett	Merge pull request #13 from alecchap/master	commit \| commitdiff \| tree
2011-06-28	derek	Added unique-alignment checks for ResolveTool	commit \| commitdiff \| tree
2011-06-23	derek	Fixed -fPIC issue for CentOS users.	commit \| commitdiff \| tree
2011-06-17	derek	Removed pessimistic warnings when jumping to regions...	commit \| commitdiff \| tree
2011-06-17	derek	Added re-calculation of BamAlignment's BinID during	commit \| commitdiff \| tree
2011-06-14	derek	Implemented better coupling of unmapped reads with...	commit \| commitdiff \| tree
2011-06-14	derek	Further fixes for ISIZE-handling in ResolveTool	commit \| commitdiff \| tree
2011-06-13	derek	Fixed some signed/unsigned InsertSize bugs in ResolveTool	commit \| commitdiff \| tree
2011-06-11	derek	ConvertTool fix: removed extra space in (BAM->FASTA...	commit \| commitdiff \| tree
2011-06-11	derek	Created 3 modes for ResolveTool: makeStats, markPairs...	commit \| commitdiff \| tree
2011-06-11	derek	Cleaned up help formatting & added some string utilities	commit \| commitdiff \| tree
2011-06-07	derek	Added new ResolveTool - for paired-end resolution....	commit \| commitdiff \| tree
2011-06-07	derek	Minor cleanup to toolkit code formatting.	commit \| commitdiff \| tree
2011-05-10	derek	Fixed minimum offset error in BAI jumping	commit \| commitdiff \| tree
2011-05-05	Derek Barnett	Merge pull request #9 from bookest/patch-1	commit \| commitdiff \| tree
2011-04-27	derek	Removed debug statements that snuck into last commit	commit \| commitdiff \| tree
2011-04-27	derek	Fixed regression bug in index formats. Wasn't properly...	commit \| commitdiff \| tree
2011-04-22	derek	Additional attempt to force -fPIC on CentOS	commit \| commitdiff \| tree
2011-04-22	derek	Modified BamAlignment in attempt to resolve symbol...	commit \| commitdiff \| tree
2011-04-19	derek	Brought API up to compliance with recent SAM Format...	commit \| commitdiff \| tree
2011-04-05	derek	Rolled back the BGZF buffer size to the original 64K...	commit \| commitdiff \| tree
2011-04-05	derek	Major performance boost to startup & random-access...	commit \| commitdiff \| tree
2011-03-23	derek	Updated Doxyfile, attempt to fix online file access	commit \| commitdiff \| tree
2011-03-23	derek	Major update to BamTools version 1.0	commit \| commitdiff \| tree
2011-02-24	derek	Attempt to fix SamHeaderVersion compile bug	commit \| commitdiff \| tree
2011-01-19	derek	Bug fix in SamHeaderVersion::SetVersion()	commit \| commitdiff \| tree
2011-01-19	derek	Missed bug fix in BamMultiMerger in early commit. Fixed...	commit \| commitdiff \| tree
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