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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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