Derek [Wed, 21 Jul 2010 15:00:44 +0000 (11:00 -0400)]
Forgot to include updated bamtools 'main' with RandomTool commmit.
Derek [Wed, 21 Jul 2010 14:48:04 +0000 (10:48 -0400)]
Added the <cctype> include to BamAux to explicitly support the toupper() fxn. It had slipped past newer compilers so far
Derek [Tue, 20 Jul 2010 22:34:31 +0000 (18:34 -0400)]
Fixed fopen-related typo in bamtools_fasta.*
Derek [Tue, 20 Jul 2010 20:28:31 +0000 (16:28 -0400)]
Added basic implementation of RandomTool. This generates a random (well, pseudo... its based on rand()) subset of alignments from BAM file(s). User can specify REGION and/or number of alignments to generate. No duplicate checking implemented. TODO: Handle BAM files without existing index - tool currently depends heavily on being able to jump around randomly
Derek [Tue, 20 Jul 2010 20:25:48 +0000 (16:25 -0400)]
Modified BamMultiReader::Open() to return bool. Still needs some tweaks to handle all error cases correctly.
Derek [Mon, 19 Jul 2010 23:05:51 +0000 (19:05 -0400)]
Added cross-platform LFS for tell/seek. Removed fopen64/freopen64 - hopefully unecessary with -D_FILE_OFFSET_BITS=64 compiler flag
Derek [Thu, 15 Jul 2010 18:04:16 +0000 (14:04 -0400)]
Fixed Rewind(). Now using LoadNextAlignment() instead of GetNextAlignmentCore(). GNAC() does region checks which, in this case of clearing prior region data, are unnecessary at best and most likely erroneous.
Derek [Thu, 15 Jul 2010 17:59:42 +0000 (13:59 -0400)]
Modified Rewind() to check actual data present when resetting region markers, instead of relying on potentially incorrect RefData::RefHasAlignments
Derek [Thu, 15 Jul 2010 17:44:53 +0000 (13:44 -0400)]
Modified handling of BamAlignmentSupportData. This fix should allow BamWriter::SaveAlignment to still handle BamAlignments retrieved using the 'standard' GetNextAlignment[Core] correctly, while adding support for BamAlignments **generated directly** in client code. Switched BASD::IsParsed to HasCoreOnly, which is false by default and only set by BamReader::GetMextAlignmentCore() - therefore the client should never to touch the BASD struct.
Derek [Tue, 13 Jul 2010 16:00:42 +0000 (12:00 -0400)]
Purely cosmetic udpate. Cleaned up some commented blocks, added file header information (author, description, etc)
Derek [Tue, 13 Jul 2010 14:47:17 +0000 (10:47 -0400)]
Updated Makefile for fasta & pileup
Derek [Tue, 13 Jul 2010 01:57:40 +0000 (21:57 -0400)]
Added support for reading FASTA sequences, as well as generating FASTA index (.fai) files. TODO: need to drop FASTA functionality into pileup conversion, as well as create command line feature to generate FASTA indices
Derek [Tue, 13 Jul 2010 01:53:57 +0000 (21:53 -0400)]
Begun basic pileup conversion
Derek [Fri, 9 Jul 2010 19:29:17 +0000 (15:29 -0400)]
Added simple PrintBed() method; plan to add PrintWiggle() next. Added use of function pointer to clean up code for conversion method selection.
Derek [Fri, 9 Jul 2010 17:02:07 +0000 (13:02 -0400)]
Fixed typos in last commit.
Derek [Fri, 9 Jul 2010 16:57:55 +0000 (12:57 -0400)]
Reorganized convert tool code. Restored stdin by default. Implemented FASTA/FASTQ convert methods. Still need to include support for new (.bti) index file format
Derek [Fri, 9 Jul 2010 16:28:22 +0000 (12:28 -0400)]
Merge http://github.com/ekg/bamtools
Derek [Fri, 9 Jul 2010 16:20:39 +0000 (12:20 -0400)]
Fixed: proper handling of BamAlignment::AlignedBases when QueryBases is empty. Thanks to Aaron Quinlan for catching this.
Derek [Fri, 9 Jul 2010 16:08:31 +0000 (12:08 -0400)]
Updated index and count sub-tools to recognize new (.bti) index file format
Derek [Fri, 9 Jul 2010 16:06:27 +0000 (12:06 -0400)]
Separated indexing ops to new class. Implemented a fixed-partition-size index format (.bti) as an alternative to the BAM default (.bai)
Derek [Fri, 9 Jul 2010 16:04:07 +0000 (12:04 -0400)]
Enforced proper handling of large files (>4Gb) on 32-bit systems.
Erik Garrison [Wed, 7 Jul 2010 19:54:39 +0000 (15:54 -0400)]
Merge BamMultiReader and SetRegion into bamtools convert
This commit merges the BamMultiReader and SetRegion method into the
conversion tool. This greatly simplifies the process of dumping
alignments from regions in a set of bam files.
Breaking in this commit: stdin input by default. To be fixed in a
subsequent commit.
Erik Garrison [Wed, 7 Jul 2010 19:32:48 +0000 (15:32 -0400)]
Remove heavy-handed failure mode in BamMultiReader::SetRegion
In practice a failure of BamReader::SetRegion means that we can't get
alignments from the specified region. It is simpler to ignore failures
of SetRegion as they are gracefully handled by UpdateAlignments, which
simply doesn't add alignments from the readers which don't have
alignments in the target region.
This resolves a bug in which bamtools count (and any other utility using
BamMultiReader::SetRegion) would crash when provided a target region
with no alignments.
Derek [Mon, 28 Jun 2010 19:14:12 +0000 (15:14 -0400)]
Removed accidental commit of .o files
Derek [Mon, 28 Jun 2010 19:10:28 +0000 (15:10 -0400)]
Modified BamReader(and BGZF)::Open() to return bool. Tried to eliminate most exit() calls. These changes should allow for more graceful error handling. Some 'code cleanup' in BW, but no logic changes.
Derek [Tue, 22 Jun 2010 03:17:38 +0000 (23:17 -0400)]
Updated temp file path stubs to reflect input BAM file stub, so that simultaneous sort runs don't interfere with each other.
Derek [Tue, 22 Jun 2010 02:23:32 +0000 (22:23 -0400)]
Rough implementation of sort tool. Generate lots of smaller sorted (STL sort with 'custom' compare fxn) temp files in one pass, using a specified buffer size. Uses BamMultiReader paired with BamWriter to re-merge all temp files back into a single output BAM, also in one pass. Some work remains on optimizing parameters (e.g. default buffer size), scalability (single pass generates lots of temp files), & parallelization to make tool more sophisticated & robust.
Erik Garrison [Mon, 21 Jun 2010 15:56:39 +0000 (11:56 -0400)]
Gracefully handle empty files with the BamMultiReader
This commit handles the case where an empty BAM file is passed in the
list of filenames given to BamMultiReader::Open(...). Now a warning is
emitted if the file contains no alignments (or cannot be opened) and the
file is ignored.
Erik Garrison [Fri, 18 Jun 2010 19:13:46 +0000 (15:13 -0400)]
integration of SetRegion into BamMultiReader
Also includes update to bamtools_count which uses the BamMultiReader by
default and no longer requires the specification of an index file on the
command line, as this would be very cumbersome to parse for multiple
input files. Added method to check for file existence using stat to
bamtools_utilities.cpp
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
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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.
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barnett [Thu, 6 May 2010 19:30:12 +0000 (19:30 +0000)]
Added BamMultiReader and BamMultiMerge
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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
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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
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barnett [Wed, 31 Mar 2010 18:41:40 +0000 (18:41 +0000)]
Updated BamAux modified date
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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
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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
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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)
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barnett [Tue, 30 Mar 2010 15:39:47 +0000 (15:39 +0000)]
Updated contact info in README
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barnett [Tue, 30 Mar 2010 15:36:55 +0000 (15:36 +0000)]
Had some typos in last commit. Fixed.
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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
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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.
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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.
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barnett [Fri, 8 Jan 2010 19:55:45 +0000 (19:55 +0000)]
Updated BamAux
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barnett [Fri, 8 Jan 2010 18:42:30 +0000 (18:42 +0000)]
Added empty block EOF to BGZF::Close
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barnett [Tue, 8 Dec 2009 19:10:52 +0000 (19:10 +0000)]
Fixed README typos
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barnett [Tue, 8 Dec 2009 19:10:18 +0000 (19:10 +0000)]
Updated README
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barnett [Tue, 8 Dec 2009 19:02:04 +0000 (19:02 +0000)]
Fixed a few more signed/unsigned issues
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barnett [Tue, 8 Dec 2009 18:57:41 +0000 (18:57 +0000)]
Fixed some signed/unsigned int issues
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barnett [Tue, 8 Dec 2009 18:42:22 +0000 (18:42 +0000)]
Updated Makefile
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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
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barnett [Thu, 1 Oct 2009 04:13:22 +0000 (04:13 +0000)]
Fix of signed/unsigned in BamReader methods
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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)
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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
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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
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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
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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.
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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
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barnett [Thu, 16 Jul 2009 15:02:14 +0000 (15:02 +0000)]
Added BamConversion back to BamTools
Updated Makefile
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