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git.donarmstrong.com Git - bamtools.git/log
Erik Garrison [Fri, 18 Jun 2010 15:31:34 +0000 (11:31 -0400)]
moved bamtools_count to use BamRegion
This is more consistent than using a bespoke struct (Region) with the
same fields.
Derek [Thu, 17 Jun 2010 21:35:27 +0000 (17:35 -0400)]
Modified Jump() scheme to take better account of specified region and drill down closer to region beginning. Introduced RegionState to BRP in order to allow LoadNextAlignment to quit once an alignment is found beyond region.
Derek [Thu, 17 Jun 2010 16:31:29 +0000 (12:31 -0400)]
Modified BamReaderPrivate::GetOffset() & BinsFromRegion() to make use of right bound cutoffs
Derek [Thu, 17 Jun 2010 04:01:56 +0000 (00:01 -0400)]
Added concept of a fully specified region of interest to the BamReader API. Added BamRegion struct to BamAux.h. Added SetRegion() methods to BamReader. Reorganized or modified these existing BamReaderPrivate functions: BamReaderPrivate(), Close(), GetNextAlignment/Core(), IsOverlap(), Jump(), & Rewind(). Cleans up a lot of region-checking client code.
Erik Garrison [Thu, 10 Jun 2010 17:33:28 +0000 (13:33 -0400)]
change merger to use GetNextAlignmentCore
This provides a modest performance boost to the merger. A small change
to the BamAlignment copy constructor was required (to copy
BamAlignmentSupportData).
Erik Garrison [Thu, 10 Jun 2010 13:23:36 +0000 (09:23 -0400)]
Merge branch 'master' of git://github.com/pezmaster31/bamtools
Derek [Thu, 10 Jun 2010 04:50:37 +0000 (00:50 -0400)]
Moved BamAlignmentSupportData into BamAlignment data type. This continues the read/write speedup mentioned in prior commits, but removes the need for clients to manage this additional auxilary data object. The 'BamAlignment lite' is accessed by calling BamReader::GetNextAlignmentCore() and written by BamWriter::SaveAlignment() which checks to see how much parsing & packing is needed before writing.
Erik Garrison [Wed, 9 Jun 2010 16:06:13 +0000 (12:06 -0400)]
further cleanup of duplicate @RG tag warning reporting
Erik Garrison [Wed, 9 Jun 2010 15:46:46 +0000 (11:46 -0400)]
added warning for duplicate @RG tag in header
Erik Garrison [Wed, 9 Jun 2010 13:39:07 +0000 (09:39 -0400)]
fixed potential bug with previous commit
The previous commit made assumptions about the ordering of subtags
within @RG header lines. This commit only assumes that the read group
ID is specified by "ID", thus following spec.
Erik Garrison [Wed, 9 Jun 2010 13:31:01 +0000 (09:31 -0400)]
fixed bug with @RG handling
Prior to this commit files merged with bamtools merge would have one @RG
tag for each file. This is undesirable behavior. This commit fixes the
issue by tracking unique @RG tags in our unified header
(BamMultiReader::GetHeaderText) and prevents the MultiReader from
observing more than one @RG tag in the header. Future merges will have
the correct header.
Erik Garrison [Wed, 9 Jun 2010 12:39:07 +0000 (08:39 -0400)]
Merge branch 'master' of git://github.com/pezmaster31/bamtools
Derek [Wed, 9 Jun 2010 03:42:03 +0000 (23:42 -0400)]
Removed accidental add of object files
Derek [Wed, 9 Jun 2010 03:29:45 +0000 (23:29 -0400)]
Added GetNextAlignmentCore() to BamReader API as well as a corresponding SaveAlignment() in BamWriter. Both utilitze the BamAlignmentSupportData structure which contains the raw character data and lengths, and which has been bumped to BamAux.h. Exposing these methods should allow for quicker read/writes for tools that are only concerned with alignment/positional data, not the actual sequences.
Erik Garrison [Tue, 8 Jun 2010 20:28:58 +0000 (16:28 -0400)]
BamMultiReader data structure rewrite
Rewrite to improve performance of the MultiReader on large sets of
files. Move tracking of readers, alignments, and positions from several
decoupled vectors into a single multimap, allowing rapid acquisition of
the lowest 'current' alignment among the set of open readers. Expect
some performance boost when running the MultReader on large numbers of
files, as prior to this rewrite each alignment required roughly 3 x N
ops (where N is the number of files) checking all these vectors.
Erik Garrison [Tue, 8 Jun 2010 17:05:59 +0000 (13:05 -0400)]
json output
Derek [Tue, 8 Jun 2010 16:32:02 +0000 (12:32 -0400)]
Fixed output of tag types c & C. Removed atoi() call. Simply casting the single byte to int works correctly.
Derek [Mon, 7 Jun 2010 20:18:10 +0000 (16:18 -0400)]
This fixes the out-of-range exception. Though there's still a discrepancy with some (but, maddeningly, not all) tags following a string tag. Will look into to more detail, but at least it shouldn't crash in the meantime
Erik Garrison [Mon, 7 Jun 2010 19:25:25 +0000 (15:25 -0400)]
pass ostream variable to print functions in convert
Derek [Mon, 7 Jun 2010 17:58:46 +0000 (13:58 -0400)]
Began rolling over bamtools_sam into bamtools_convert. Kinda hacky setup for now, but ok to get conversion routines tested
Derek [Mon, 7 Jun 2010 17:24:51 +0000 (13:24 -0400)]
Fixed typo in settings config.
Derek [Thu, 3 Jun 2010 20:02:51 +0000 (16:02 -0400)]
Added ConvertTool.h/cpp. Not yet implemented.
Derek [Thu, 3 Jun 2010 19:28:43 +0000 (15:28 -0400)]
Updated README
Derek [Thu, 3 Jun 2010 19:27:02 +0000 (15:27 -0400)]
Added FilterTool.h/cpp. Not yet implemented.
Derek [Thu, 3 Jun 2010 17:42:31 +0000 (13:42 -0400)]
Added a second Utilities::ParseRegionString() that accepts BamMultiReader
Derek [Thu, 3 Jun 2010 17:34:13 +0000 (13:34 -0400)]
Cleaned up CountTool, by extending Utilities::ParseRegionString() to also do validation. Should be useful for other tools using REGION strings
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.
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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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