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git.donarmstrong.com Git - bamtools.git/log
Derek [Thu, 3 Jun 2010 16:30:15 +0000 (12:30 -0400)]
Minor formatting/commenting fixes. No major changes to actual code paths
Derek [Thu, 3 Jun 2010 03:52:07 +0000 (23:52 -0400)]
Implemented bamtools sam. Required new unpack methods in BGZF.h. Seems to pass all files tested, compared against samtools view output
Derek [Wed, 2 Jun 2010 18:22:57 +0000 (14:22 -0400)]
Removed a debug output statement that piggybacked into the last commit
Derek [Wed, 2 Jun 2010 18:13:24 +0000 (14:13 -0400)]
Implemented CountTool, cleaned up MergeTool.
Derek [Wed, 2 Jun 2010 16:06:43 +0000 (12:06 -0400)]
Put utilities into own class with static methods
Derek [Wed, 2 Jun 2010 02:54:30 +0000 (22:54 -0400)]
Implemented Mosaik-style command line parser, instead of former GetOpt parser. Setup an AbstractTool base class for all subtools. Split tools into .h/.cpp pairs
Derek [Thu, 27 May 2010 02:25:39 +0000 (22:25 -0400)]
Mostly cleaned up help & usage messages. Added MIT license.
Derek [Wed, 26 May 2010 20:17:14 +0000 (16:17 -0400)]
Removed BamTrimMain.cpp. Missed that one in last commit, removing the old 'toy' examples
Derek [Wed, 26 May 2010 20:16:03 +0000 (16:16 -0400)]
Removed BamConversionMain.cpp and BamDumpMain.cpp. No longer needed if toolkit available.
Derek [Wed, 26 May 2010 20:09:15 +0000 (16:09 -0400)]
Removed bamtools_test from Makefile. Was a temporary, local test harness only
Derek [Wed, 26 May 2010 20:05:15 +0000 (16:05 -0400)]
Reorganization of toolkit. Split subtools out to own headers. Added custom getopt functionality for subtools arguments. Provided or extended rough implementations for most subtools.
Derek [Tue, 25 May 2010 17:12:27 +0000 (13:12 -0400)]
Added templated GetTag() method, compile tested, but not runtime tested
Erik Garrison [Fri, 21 May 2010 21:07:31 +0000 (17:07 -0400)]
Complete prior commit
In this commit, addition of verification that reference sequences
are identical among readers opened by the BamMultiReader. Without this
check the behavior of the MultiReader is undefined.
Erik Garrison [Fri, 21 May 2010 20:53:26 +0000 (16:53 -0400)]
bamtools executable
Merge a number of useful tools into a single executable.
Also in this commit, addition of verification that reference sequences
are identical among readers opened by the BamMultiReader. Without this
check the behavior of the MultiReader is undefined.
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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