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Erik Garrison [Fri, 21 May 2010 21:07:31 +0000 (17:07 -0400)]
Complete prior commit
Erik Garrison [Fri, 21 May 2010 20:53:26 +0000 (16:53 -0400)]
bamtools executable
barnett [Fri, 7 May 2010 21:15:38 +0000 (21:15 +0000)]
Removed Boost dependency in BamMultiReader.cpp
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@52
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barnett [Fri, 7 May 2010 03:10:38 +0000 (03:10 +0000)]
Didnt actually add BamMultiMerge and BamMultiReader with last commit. Adding to repository this time, seriously.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@51
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barnett [Thu, 6 May 2010 19:30:12 +0000 (19:30 +0000)]
Added BamMultiReader and BamMultiMerge
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@50
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barnett [Wed, 14 Apr 2010 16:32:52 +0000 (16:32 +0000)]
Moved BamReaderPrivate::CalculateAlignmentEnd() to BamAlignment::GetEndPosition() to expose it to the public API. Reorganized BamAux.h to look cleaner and facilitate quick lookup of available data and methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@49
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barnett [Tue, 6 Apr 2010 19:30:32 +0000 (19:30 +0000)]
Major speedup of BamReader - removed full character data building until alignment actually requested
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@48
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barnett [Wed, 31 Mar 2010 18:41:40 +0000 (18:41 +0000)]
Updated BamAux modified date
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@47
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barnett [Wed, 31 Mar 2010 18:37:25 +0000 (18:37 +0000)]
Restored BamDumpMain to old version without dumping tag data
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@46
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barnett [Wed, 31 Mar 2010 18:36:11 +0000 (18:36 +0000)]
Major fix in handling tag data in BamAux.h... checking for null characters in BamAlignment::GetReadGroup() and similar methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@45
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barnett [Wed, 31 Mar 2010 17:54:16 +0000 (17:54 +0000)]
Major dumb fix in BamAux.h BamAlignment::SkipToNextTag() - float values are 4 bytes, not 2... moved case statement
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@44
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barnett [Wed, 31 Mar 2010 17:40:13 +0000 (17:40 +0000)]
Modified BamDump to spit out TagData (for debugging)
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@43
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barnett [Tue, 30 Mar 2010 15:39:47 +0000 (15:39 +0000)]
Updated contact info in README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@42
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barnett [Tue, 30 Mar 2010 15:36:55 +0000 (15:36 +0000)]
Had some typos in last commit. Fixed.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@41
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barnett [Tue, 30 Mar 2010 15:00:57 +0000 (15:00 +0000)]
Fixed: off by 1 in BamWriter, variable tag parsing in BamAux, endian-correctness
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@40
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barnett [Mon, 11 Jan 2010 19:10:15 +0000 (19:10 +0000)]
Added #include<cstdio> to BamAux.h to cover use of printf. Added AlignmentFlag setter methods, per request by Aaron.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@39
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barnett [Mon, 11 Jan 2010 15:11:15 +0000 (15:11 +0000)]
Fixed fread() related compiler warnings. Fixed std types [u]intX_t errors (used, but not defined in BamAux.h). Added Aaron's stdin/stdout read/write feature.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@38
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barnett [Fri, 8 Jan 2010 19:55:45 +0000 (19:55 +0000)]
Updated BamAux
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@37
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barnett [Fri, 8 Jan 2010 18:42:30 +0000 (18:42 +0000)]
Added empty block EOF to BGZF::Close
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@36
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barnett [Tue, 8 Dec 2009 19:10:52 +0000 (19:10 +0000)]
Fixed README typos
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@35
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barnett [Tue, 8 Dec 2009 19:10:18 +0000 (19:10 +0000)]
Updated README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@34
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barnett [Tue, 8 Dec 2009 19:02:04 +0000 (19:02 +0000)]
Fixed a few more signed/unsigned issues
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@33
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barnett [Tue, 8 Dec 2009 18:57:41 +0000 (18:57 +0000)]
Fixed some signed/unsigned int issues
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@32
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barnett [Tue, 8 Dec 2009 18:42:22 +0000 (18:42 +0000)]
Updated Makefile
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@31
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barnett [Tue, 8 Dec 2009 18:37:03 +0000 (18:37 +0000)]
Major overhaul to BamTools
Separated out Bgzf routines to BGZF.h
Simplified main BamReader.h/BamWriter.h headers, by adding pimpl
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@30
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barnett [Thu, 1 Oct 2009 04:13:22 +0000 (04:13 +0000)]
Fix of signed/unsigned in BamReader methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@29
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barnett [Thu, 1 Oct 2009 04:11:55 +0000 (04:11 +0000)]
Modified BamAlignment data members to match BAM specs (signed vs unsigned ints)
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@28
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barnett [Wed, 30 Sep 2009 16:55:07 +0000 (16:55 +0000)]
changed SIZEOF_INT to BT_SIZEOF_INT - namespace collision on Xcode-GCC
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@27
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barnett [Fri, 25 Sep 2009 17:59:46 +0000 (17:59 +0000)]
Changed BamAlignment::InsertSize to signed int... need to test
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@26
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barnett [Thu, 17 Sep 2009 22:02:24 +0000 (22:02 +0000)]
Changed BGZF data member to pointer... to force buffer clean out with new/delete on reader open/close
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@25
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mikaels [Tue, 4 Aug 2009 20:44:19 +0000 (20:44 +0000)]
fixed a bug where the terminal null wasn't being saved in SaveAlignment.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@24
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barnett [Thu, 16 Jul 2009 15:08:20 +0000 (15:08 +0000)]
Changed BAM_CORE_SIZE to unsigned int to remove signed comparison warning in BamReader.cpp:543
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@23
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barnett [Thu, 16 Jul 2009 15:02:14 +0000 (15:02 +0000)]
Added BamConversion back to BamTools
Updated Makefile
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@22
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barnett [Wed, 15 Jul 2009 18:06:13 +0000 (18:06 +0000)]
Updated README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@21
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barnett [Wed, 15 Jul 2009 18:02:28 +0000 (18:02 +0000)]
Full update to SVN after combining BamReader and BamWriter into cohesive BamTools API.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@20
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barnett [Mon, 18 May 2009 16:25:20 +0000 (16:25 +0000)]
Major overhaul of BamReader. No longer relying on bgzf.* API. Sped up random-access. STLUtilities.h no longer needed
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@19
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barnett [Thu, 23 Apr 2009 20:33:56 +0000 (20:33 +0000)]
Had signs reversed in GetOffset error check. Fixed
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@18
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barnett [Thu, 23 Apr 2009 20:26:30 +0000 (20:26 +0000)]
Removed assertion in GetOffset(), now returns -1 if regionChunks == 0. Jump() then returns false if offset = -1, else tries to Jump
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@17
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barnett [Sun, 19 Apr 2009 20:39:29 +0000 (20:39 +0000)]
Bug fix in BamMerge.cpp by Chip
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@16
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barnett [Mon, 13 Apr 2009 15:17:17 +0000 (15:17 +0000)]
Chip - removed limits
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@15
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barnett [Mon, 13 Apr 2009 13:45:48 +0000 (13:45 +0000)]
Added Chip's BamMerge to the repository
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@14
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mikaels [Sat, 11 Apr 2009 03:45:55 +0000 (03:45 +0000)]
Fixed some of the output for tag data.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@13
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mikaels [Sat, 11 Apr 2009 03:45:39 +0000 (03:45 +0000)]
Forgot some include statements.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@12
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mikaels [Sat, 11 Apr 2009 03:32:53 +0000 (03:32 +0000)]
Added tag data support.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@11
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mikaels [Sat, 11 Apr 2009 03:31:59 +0000 (03:31 +0000)]
Added support for the tag data and provided a GetReadGroup accessor.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@10
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mikaels [Sat, 11 Apr 2009 01:25:31 +0000 (01:25 +0000)]
removed DOS line endings
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@9
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mikaels [Fri, 10 Apr 2009 18:03:14 +0000 (18:03 +0000)]
Removed the profiling options since they shouldn't be standard.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@8
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mikaels [Fri, 10 Apr 2009 18:00:26 +0000 (18:00 +0000)]
Made many improvements to the code that pass the stricter syntax checking in Visual Studio.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@7
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mikaels [Fri, 10 Apr 2009 17:59:34 +0000 (17:59 +0000)]
Updated the header text to give credit to the Broad Institute for the bgzf routines.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@6
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mikaels [Fri, 10 Apr 2009 17:59:00 +0000 (17:59 +0000)]
Defined some of the non-standard data types for compatibility with Visual Studio.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@5
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mikaels [Fri, 10 Apr 2009 16:06:39 +0000 (16:06 +0000)]
Added BamConversion to the make clean command
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@4
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barnett [Fri, 10 Apr 2009 15:26:37 +0000 (15:26 +0000)]
Updated BamReaderMain.cpp to remove unused variable warnings from compile.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@3
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mikaels [Fri, 10 Apr 2009 15:07:49 +0000 (15:07 +0000)]
Initial import.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@2
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barnett [Fri, 10 Apr 2009 15:06:28 +0000 (15:06 +0000)]
creating directories
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@1
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