projects
/
bamtools.git
/ shortlog
commit
grep
author
committer
pickaxe
?
search:
re
summary
| shortlog |
log
|
commit
|
commitdiff
|
tree
first ⋅ prev ⋅
next
bamtools.git
2010-07-21
Derek
Forgot to include updated bamtools 'main' with RandomTo...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-21
Derek
Added the <cctype> include to BamAux to explicitly...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-20
Derek
Fixed fopen-related typo in bamtools_fasta.*
commit
|
commitdiff
|
tree
|
snapshot
2010-07-20
Derek
Added basic implementation of RandomTool. This generate...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-20
Derek
Modified BamMultiReader::Open() to return bool. Still...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-19
Derek
Added cross-platform LFS for tell/seek. Removed fopen64...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-15
Derek
Fixed Rewind(). Now using LoadNextAlignment() instead...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-15
Derek
Modified Rewind() to check actual data present when...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-15
Derek
Modified handling of BamAlignmentSupportData. This...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-13
Derek
Purely cosmetic udpate. Cleaned up some commented block...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-13
Derek
Updated Makefile for fasta & pileup
commit
|
commitdiff
|
tree
|
snapshot
2010-07-13
Derek
Added support for reading FASTA sequences, as well...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-13
Derek
Begun basic pileup conversion
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Added simple PrintBed() method; plan to add PrintWiggle...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Fixed typos in last commit.
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Reorganized convert tool code. Restored stdin by defaul...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Merge http://github.com/ekg/bamtools
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Fixed: proper handling of BamAlignment::AlignedBases...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Updated index and count sub-tools to recognize new...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Separated indexing ops to new class. Implemented a...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-09
Derek
Enforced proper handling of large files (>4Gb) on 32...
commit
|
commitdiff
|
tree
|
snapshot
2010-07-07
Erik Garrison
Merge BamMultiReader and SetRegion into bamtools convert
commit
|
commitdiff
|
tree
|
snapshot
2010-07-07
Erik Garrison
Remove heavy-handed failure mode in BamMultiReader...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-28
Derek
Removed accidental commit of .o files
commit
|
commitdiff
|
tree
|
snapshot
2010-06-28
Derek
Modified BamReader(and BGZF)::Open() to return bool...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-22
Derek
Updated temp file path stubs to reflect input BAM file...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-22
Derek
Rough implementation of sort tool. Generate lots of...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-21
Erik Garrison
Gracefully handle empty files with the BamMultiReader
commit
|
commitdiff
|
tree
|
snapshot
2010-06-18
Erik Garrison
integration of SetRegion into BamMultiReader
commit
|
commitdiff
|
tree
|
snapshot
2010-06-18
Erik Garrison
moved bamtools_count to use BamRegion
commit
|
commitdiff
|
tree
|
snapshot
2010-06-17
Derek
Modified Jump() scheme to take better account of specif...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-17
Derek
Modified BamReaderPrivate::GetOffset() & BinsFromRegion...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-17
Derek
Added concept of a fully specified region of interest...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-10
Erik Garrison
change merger to use GetNextAlignmentCore
commit
|
commitdiff
|
tree
|
snapshot
2010-06-10
Erik Garrison
Merge branch 'master' of git://github.com/pezmaster31...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-10
Derek
Moved BamAlignmentSupportData into BamAlignment data...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Erik Garrison
further cleanup of duplicate @RG tag warning reporting
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Erik Garrison
added warning for duplicate @RG tag in header
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Erik Garrison
fixed potential bug with previous commit
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Erik Garrison
fixed bug with @RG handling
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Erik Garrison
Merge branch 'master' of git://github.com/pezmaster31...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Derek
Removed accidental add of object files
commit
|
commitdiff
|
tree
|
snapshot
2010-06-09
Derek
Added GetNextAlignmentCore() to BamReader API as well...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-08
Erik Garrison
BamMultiReader data structure rewrite
commit
|
commitdiff
|
tree
|
snapshot
2010-06-08
Erik Garrison
json output
commit
|
commitdiff
|
tree
|
snapshot
2010-06-08
Derek
Fixed output of tag types c & C. Removed atoi() call...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-07
Derek
This fixes the out-of-range exception. Though there...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-07
Erik Garrison
pass ostream variable to print functions in convert
commit
|
commitdiff
|
tree
|
snapshot
2010-06-07
Derek
Began rolling over bamtools_sam into bamtools_convert...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-07
Derek
Fixed typo in settings config.
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Added ConvertTool.h/cpp. Not yet implemented.
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Updated README
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Added FilterTool.h/cpp. Not yet implemented.
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Added a second Utilities::ParseRegionString() that...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Cleaned up CountTool, by extending Utilities::ParseRegi...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Minor formatting/commenting fixes. No major changes...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-03
Derek
Implemented bamtools sam. Required new unpack methods...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-02
Derek
Removed a debug output statement that piggybacked into...
commit
|
commitdiff
|
tree
|
snapshot
2010-06-02
Derek
Implemented CountTool, cleaned up MergeTool.
commit
|
commitdiff
|
tree
|
snapshot
2010-06-02
Derek
Put utilities into own class with static methods
commit
|
commitdiff
|
tree
|
snapshot
2010-06-02
Derek
Implemented Mosaik-style command line parser, instead...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-27
Derek
Mostly cleaned up help & usage messages. Added MIT...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-26
Derek
Removed BamTrimMain.cpp. Missed that one in last commit...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-26
Derek
Removed BamConversionMain.cpp and BamDumpMain.cpp....
commit
|
commitdiff
|
tree
|
snapshot
2010-05-26
Derek
Removed bamtools_test from Makefile. Was a temporary...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-26
Derek
Reorganization of toolkit. Split subtools out to own...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-25
Derek
Added templated GetTag() method, compile tested, but...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-21
Erik Garrison
Complete prior commit
commit
|
commitdiff
|
tree
|
snapshot
2010-05-21
Erik Garrison
bamtools executable
commit
|
commitdiff
|
tree
|
snapshot
2010-05-07
barnett
Removed Boost dependency in BamMultiReader.cpp
commit
|
commitdiff
|
tree
|
snapshot
2010-05-07
barnett
Didnt actually add BamMultiMerge and BamMultiReader...
commit
|
commitdiff
|
tree
|
snapshot
2010-05-06
barnett
Added BamMultiReader and BamMultiMerge
commit
|
commitdiff
|
tree
|
snapshot
2010-04-14
barnett
Moved BamReaderPrivate::CalculateAlignmentEnd() to...
commit
|
commitdiff
|
tree
|
snapshot
2010-04-06
barnett
Major speedup of BamReader - removed full character...
commit
|
commitdiff
|
tree
|
snapshot
2010-03-31
barnett
Updated BamAux modified date
commit
|
commitdiff
|
tree
|
snapshot
2010-03-31
barnett
Restored BamDumpMain to old version without dumping...
commit
|
commitdiff
|
tree
|
snapshot
2010-03-31
barnett
Major fix in handling tag data in BamAux.h... checking...
commit
|
commitdiff
|
tree
|
snapshot
2010-03-31
barnett
Major dumb fix in BamAux.h BamAlignment::SkipToNextTag...
commit
|
commitdiff
|
tree
|
snapshot
2010-03-31
barnett
Modified BamDump to spit out TagData (for debugging)
commit
|
commitdiff
|
tree
|
snapshot
2010-03-30
barnett
Updated contact info in README
commit
|
commitdiff
|
tree
|
snapshot
2010-03-30
barnett
Had some typos in last commit. Fixed.
commit
|
commitdiff
|
tree
|
snapshot
2010-03-30
barnett
Fixed: off by 1 in BamWriter, variable tag parsing...
commit
|
commitdiff
|
tree
|
snapshot
2010-01-11
barnett
Added #include<cstdio> to BamAux.h to cover use of...
commit
|
commitdiff
|
tree
|
snapshot
2010-01-11
barnett
Fixed fread() related compiler warnings. Fixed std...
commit
|
commitdiff
|
tree
|
snapshot
2010-01-08
barnett
Updated BamAux
commit
|
commitdiff
|
tree
|
snapshot
2010-01-08
barnett
Added empty block EOF to BGZF::Close
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Fixed README typos
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Updated README
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Fixed a few more signed/unsigned issues
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Fixed some signed/unsigned int issues
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Updated Makefile
commit
|
commitdiff
|
tree
|
snapshot
2009-12-08
barnett
Major overhaul to BamTools
commit
|
commitdiff
|
tree
|
snapshot
2009-10-01
barnett
Fix of signed/unsigned in BamReader methods
commit
|
commitdiff
|
tree
|
snapshot
2009-10-01
barnett
Modified BamAlignment data members to match BAM specs...
commit
|
commitdiff
|
tree
|
snapshot
2009-09-30
barnett
changed SIZEOF_INT to BT_SIZEOF_INT - namespace collisi...
commit
|
commitdiff
|
tree
|
snapshot
2009-09-25
barnett
Changed BamAlignment::InsertSize to signed int... need...
commit
|
commitdiff
|
tree
|
snapshot
2009-09-17
barnett
Changed BGZF data member to pointer... to force buffer...
commit
|
commitdiff
|
tree
|
snapshot
2009-08-04
mikaels
fixed a bug where the terminal null wasn't being saved...
commit
|
commitdiff
|
tree
|
snapshot
2009-07-16
barnett
Changed BAM_CORE_SIZE to unsigned int to remove signed...
commit
|
commitdiff
|
tree
|
snapshot
2009-07-16
barnett
Added BamConversion back to BamTools
commit
|
commitdiff
|
tree
|
snapshot
next