[med-svn] [SCM] bamtools annotated tag, upstream/2.2.1, created. upstream/2.2.1
Charles Plessy
plessy at debian.org
Mon Apr 1 06:59:25 UTC 2013
The annotated tag, upstream/2.2.1 has been created
at ae366ff9bfa3f78715d00455adf4bf1a8b69325b (tag)
tagging ed194043ff8f3563a942307ba79bf8980a6a6981 (commit)
tagged by Charles Plessy
on Mon Apr 1 15:28:55 2013 +0900
- Shortlog ------------------------------------------------------------
Upstream version 2.2.1
Alec Chapman (1):
Fix Visual Studio compiler errors.
Charles Plessy (1):
Imported Upstream version 2.2.1
Chase Miller (1):
Added Yaml for outputing BamAlignments.
Christopher Grim (1):
'make install' should install bin/bamtools
Derek (120):
Added templated GetTag() method, compile tested, but not runtime tested
Reorganization of toolkit. Split subtools out to own headers. Added custom getopt functionality for subtools arguments. Provided or extended rough implementations for most subtools.
Removed bamtools_test from Makefile. Was a temporary, local test harness only
Removed BamConversionMain.cpp and BamDumpMain.cpp. No longer needed if toolkit available.
Removed BamTrimMain.cpp. Missed that one in last commit, removing the old 'toy' examples
Mostly cleaned up help & usage messages. Added MIT license.
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
Put utilities into own class with static methods
Implemented CountTool, cleaned up MergeTool.
Removed a debug output statement that piggybacked into the last commit
Implemented bamtools sam. Required new unpack methods in BGZF.h. Seems to pass all files tested, compared against samtools view output
Minor formatting/commenting fixes. No major changes to actual code paths
Cleaned up CountTool, by extending Utilities::ParseRegionString() to also do validation. Should be useful for other tools using REGION strings
Added a second Utilities::ParseRegionString() that accepts BamMultiReader
Added FilterTool.h/cpp. Not yet implemented.
Updated README
Added ConvertTool.h/cpp. Not yet implemented.
Fixed typo in settings config.
Began rolling over bamtools_sam into bamtools_convert. Kinda hacky setup for now, but ok to get conversion routines tested
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
Fixed output of tag types c & C. Removed atoi() call. Simply casting the single byte to int works correctly.
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.
Removed accidental add of object files
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.
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.
Modified BamReaderPrivate::GetOffset() & BinsFromRegion() to make use of right bound cutoffs
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.
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.
Updated temp file path stubs to reflect input BAM file stub, so that simultaneous sort runs don't interfere with each other.
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.
Removed accidental commit of .o files
Enforced proper handling of large files (>4Gb) on 32-bit systems.
Separated indexing ops to new class. Implemented a fixed-partition-size index format (.bti) as an alternative to the BAM default (.bai)
Updated index and count sub-tools to recognize new (.bti) index file format
Fixed: proper handling of BamAlignment::AlignedBases when QueryBases is empty. Thanks to Aaron Quinlan for catching this.
Merge http://github.com/ekg/bamtools
Reorganized convert tool code. Restored stdin by default. Implemented FASTA/FASTQ convert methods. Still need to include support for new (.bti) index file format
Fixed typos in last commit.
Added simple PrintBed() method; plan to add PrintWiggle() next. Added use of function pointer to clean up code for conversion method selection.
Begun basic pileup conversion
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
Updated Makefile for fasta & pileup
Purely cosmetic udpate. Cleaned up some commented blocks, added file header information (author, description, etc)
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.
Modified Rewind() to check actual data present when resetting region markers, instead of relying on potentially incorrect RefData::RefHasAlignments
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.
Added cross-platform LFS for tell/seek. Removed fopen64/freopen64 - hopefully unecessary with -D_FILE_OFFSET_BITS=64 compiler flag
Modified BamMultiReader::Open() to return bool. Still needs some tweaks to handle all error cases correctly.
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
Fixed fopen-related typo in bamtools_fasta.*
Added the <cctype> include to BamAux to explicitly support the toupper() fxn. It had slipped past newer compilers so far
Forgot to include updated bamtools 'main' with RandomTool commmit.
Fixed: remove unnecessary EOF write attempt for read-only files in BGZF::Close()
Fixed variable length tag data retrieval in BamAlignment::GetTag(). To do this, removed templated GetTag(). Now have explicit overridden string, unsigned int, signed int, and float flavors of the method.
Removed SamTool (bamtools sam ...) from toolkit. This functionality is covered by ConvertTool.
Forgot to update Makefile with last commit
Various cleanups. Added -noheader to SAM conversion in ConvertTool
Implemented basic alignment stats (count/%) for most of the alignment flags
Mostly cosmetic fixes. A few tweaks to subtool options/settings naming or default handling as well.
Reworded bamtools stats general help description
Added AddTag/EditTag/RemoveTag methods to BamAlignment. Refactored existing GetTag methods.
Bug fix in BamReader::Jump()
Minor formatting cleanup: really just an update to be able to pull in Erik's JSON changes.
Merge git://github.com/ekg/bamtools
Added write-uncompressed flag to BGZF. Commit includes some other formatting cleanup as well.
Modified BamWriter::Open() to return bool on success/fail - was silent before, so clients had no way of handling errors
Modified the way BGZF sets up uncompressed output. Modified BamWriter to support uncompressed option.
Minor formatting cleanup in BamIndex.*
Reorganized source tree & build system
Modified Makefile to ensure creation of bin/ and obj/ directories
Added simple header comments to all Makefiles, to help distinguish between them easier
Missed a Makefile in last commit - just adding header comments
Added JsonCPP code to repo. Will be used by FilterTool for script parsing
Fixed: Calls to GetEndPosition() rely on CIGAR data being parsed. Previously this was not set if BamAlignment was retrieved via GetNextAlignmentCore(). Moved CIGAR parsing back to LoadNextAlignment() to ensure this works properly.
Forgot to add jsoncpp/json.h in a previous commit
Removed -pg debug flag from Makefile CXXFLAGS, accidentally incorporated into a prior commit
Added bamtools_filter_engine.*
Updating bamtools_options
Updated bamtools_utilities with #defines
Minor formatting & commenting update
Posted implementation of FilterTool.
Added uncompressed output as default behavior for Filter-, Merge-, and RandomTools when sending results to stdout. User can override this behavior using the command line option: -forceCompression
Modified help description for -bti option
Added IsIndexLoaded() public method to BamReader. Allows client to make sure index data is available before attempting any random access ops
Cleaned up index file handling throughout toolkit. Did this by adding a FileExists() methods to BamMultiReader for determining which index file to load.
Modified Utilities::FileExists() so it doesnt rely on sys/stat.h. While this header is de facto provided and supported on *most* systems, it really is not standard C/C++, so cant be trusted to be fully portable.
Large-scale API indexing re-organization:
Previously missed a line in BamReader.cpp with the recent index overhaul.
Added -region option to bamtools_merge
Documentation update
Relicensed the source code used in bamtools_options. Most of it derived from Mosaik source, which was originally released under GPL. Now under MIT License with author's permission. This puts the entire BamTools codebase securely under one unrestrictive license.
Reorganizing index/jumping calls. Now all BamReader cares about is sending a Jump() request to a BamIndex with a desired region and receiving a success/fail flag. BamIndex-derived classes will now handle all index-format-specific offset calculation, overlap checking, etc and make sure its associated BGZF stream has seek-ed as close to the desired region as that index scheme allows.
Removed debug output statement that slipped into last commit.
Reimplemented BamToolsIndex for bug fix and performance upgrade. *** NOTE *** This commit invalidats any previous BamToolsIndex files (.bti). Please re-run 'bamtools index -bti -in <yourBam>' to generate the new index files.
Fixed off-by-one error in BamAlignment::GetEndPosition()
Added option for users to specifiy half-open (1-based) return value for BamAlignment::GetEndPosition(). By default, returns 0-based coordinate after recent modification.
Added new PileupEngine to the toolkit. This is used by CoverageTool as well as ConvertTool for pileup format. Pileup conversion output before was buggy and overall incorrect. Now should match SAMtools output to the best of my knowledge
Missed an update to BamToolsIndex code in a previous commit
Did some housekeeping in BamAux.h - moved some constants to the files where they are actually used.
On second thought, moved the (non-indexing) constants back to BamAux.h, since they are not technically specific to BamWriter only and clients may be using them in their code
Fixed: bug related to accessing data (or regions with no alignments) near the ends of references, when using .bti index files. Required modifying the BamToolsIndex build step. *NOTE: This update invalidates any existing .bti files, please re-generate any that you have currently.* Versioning system in BTI will not allow users to use the older, buggy version... so no chance of accidental usage.
Moved BamAlignment data structure out to its own .h/.cpp. BamAux.h was getting over-crowded. *NOTE - This means that if you were using the BamAlignment data structure in code without a reader/writer, you need to include BamAlignment.h instead of BamAux.h. If your code was using reader/writer, no changes should be necessary on your end.
Missed api/Makefile in last commit.
Updated to match new BamAlignment.h includes
Added GetTagType() to BamAlignment
Added implementation of new SplitTool. This tool splits a single BAM file into multiple BAMs, based on a user-specified property. For now, properties supported are mapped/unmapped, paired/unpaired, split by reference, and split based on a given tag.
Removed a backup text file that snuck into an earlier commit
Cleaned up SplitTool internal implementation. Use of template methods should make maintenance a bit easier.
Implemented 'compound rule' logic in the FilterTool's script support.
Fixed lack of reverse complemented output in BAM -> FASTA/Q conversion.
Minor formatting, commenting cleanup
Fixed: bug(s) related to empty references and regions.
Changed BamAlignment::SupportData from private to public.
modified/clarified some help & usage messages
Implemented index cache mode for both BAI & BTI formats
Implemented index cache mode for both BAI & BTI formats
Merge branch 'master' of git://github.com/pezmaster31/bamtools
Fixed NoIndexCaching behavior
Updating README... still a work in progress
Merge branch 'master' of git://github.com/ekg/bamtools
Derek Barnett (9):
Merge pull request #9 from bookest/patch-1
Merge pull request #13 from alecchap/master
Merge pull request #15 from gabeiscoding/patch-1
Merge pull request #16 from gabeiscoding/patch-2
Merge pull request #39 from leecbaker/master
Merge pull request #40 from tobiasmarschall/master
Merge pull request #41 from tobiasmarschall/master
Version 2.2
Merge branch 'master' of https://github.com/pezmaster31/bamtools
Erik Garrison (36):
bamtools executable
Complete prior commit
pass ostream variable to print functions in convert
json output
BamMultiReader data structure rewrite
Merge branch 'master' of git://github.com/pezmaster31/bamtools
fixed bug with @RG handling
fixed potential bug with previous commit
added warning for duplicate @RG tag in header
further cleanup of duplicate @RG tag warning reporting
Merge branch 'master' of git://github.com/pezmaster31/bamtools
change merger to use GetNextAlignmentCore
moved bamtools_count to use BamRegion
integration of SetRegion into BamMultiReader
Gracefully handle empty files with the BamMultiReader
Remove heavy-handed failure mode in BamMultiReader::SetRegion
Merge BamMultiReader and SetRegion into bamtools convert
for json output in bamtools convert
change printf's to fprint(stderr,
Merge branch 'master' of git://github.com/pezmaster31/bamtools
prefer bamtools index in BamMultiReader
Added more verbose debugging output to BamMultiReader::SetRegion
updated debugging output in BamIndex, seek vs. calculate distinction
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Merge branch 'master' of http://github.com/pezmaster31/bamtools
added reader.Open checks to a number of tools
exposes cigar string data to bamtools filter
prior commit caused bug with convert
convert: cleanup of prior fix, report if no index file found
add index caching mode setter to BamMultiReader
clarified no-index behavior in bam multi reader
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Lee Baker (1):
Fix: Comment lines in header get lost when copying a SamHeader object.
Tobias Marschall (2):
Fix uninitialized buffer in BamReaderPrivate::LoadNextAlignment
Include header sys/filio.h for SunOS. Otherwise TcpSocketEngine_unix_p.cpp does not compile because FIONREAD is not found.
barnett (40):
creating directories
Updated BamReaderMain.cpp to remove unused variable warnings from compile.
Added Chip's BamMerge to the repository
Chip - removed limits
Bug fix in BamMerge.cpp by Chip
Removed assertion in GetOffset(), now returns -1 if regionChunks == 0. Jump() then returns false if offset = -1, else tries to Jump
Had signs reversed in GetOffset error check. Fixed
Major overhaul of BamReader. No longer relying on bgzf.* API. Sped up random-access. STLUtilities.h no longer needed
Full update to SVN after combining BamReader and BamWriter into cohesive BamTools API.
Updated README
Added BamConversion back to BamTools
Changed BAM_CORE_SIZE to unsigned int to remove signed comparison warning in BamReader.cpp:543
Changed BGZF data member to pointer... to force buffer clean out with new/delete on reader open/close
Changed BamAlignment::InsertSize to signed int... need to test
changed SIZEOF_INT to BT_SIZEOF_INT - namespace collision on Xcode-GCC
Modified BamAlignment data members to match BAM specs (signed vs unsigned ints)
Fix of signed/unsigned in BamReader methods
Major overhaul to BamTools
Updated Makefile
Fixed some signed/unsigned int issues
Fixed a few more signed/unsigned issues
Updated README
Fixed README typos
Added empty block EOF to BGZF::Close
Updated BamAux
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.
Added #include<cstdio> to BamAux.h to cover use of printf. Added AlignmentFlag setter methods, per request by Aaron.
Fixed: off by 1 in BamWriter, variable tag parsing in BamAux, endian-correctness
Had some typos in last commit. Fixed.
Updated contact info in README
Modified BamDump to spit out TagData (for debugging)
Major dumb fix in BamAux.h BamAlignment::SkipToNextTag() - float values are 4 bytes, not 2... moved case statement
Major fix in handling tag data in BamAux.h... checking for null characters in BamAlignment::GetReadGroup() and similar methods
Restored BamDumpMain to old version without dumping tag data
Updated BamAux modified date
Major speedup of BamReader - removed full character data building until alignment actually requested
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
Added BamMultiReader and BamMultiMerge
Didnt actually add BamMultiMerge and BamMultiReader with last commit. Adding to repository this time, seriously.
Removed Boost dependency in BamMultiReader.cpp
derek (140):
Reviewed BAM to YAML conversion contribution (thank you Chase Miller). Reorganized to fit BT code style & structure.
Added tag support in filter tool.
Updated README
Updated BamTools version information.
Removed non-standard stl::map method calls
Merge branch 'master' of git://github.com/ekg/bamtools
Removed more non-standard STL calls from BamIndex.cpp
Minor formatting cleanup
Changed GetNextAlignmentCore() calls to GetNextAlignment() in FilterTool
Migrated to CMake build system.
Removed commented (library export) definitions from utils & jsoncpp CMakeLists files
Added API_EXPORT macro to classes in BamTools API
Added UTILS_EXPORT macro to classes in BamTools utility library
Extracted BamReaderPrivate & BamWriterPrivate from inner classes.
Continued breaking up of monolithic classes: extracted BamStandardIndex & BamToolsIndex into their own source files.
Fixed BamRegion bug: previously only checked if refID was -1, needed to make sure all negative values were invalid
Added proper import of bamtools version info from CMake
Moved private implementation API files to internal directory for clearer separation. These should not be included by client code
Fixed: bug in the BamReader::Jump() codepath, specifically the
Added new RevertTool to the toolkit
Fixed: core mode setting for BamMultiReader::Open() in FilterTool
Fixed : improper exit code from FilterTool
Fixed: handling BamAlignments with limited char data
Made BamAlignment flag queries symmetrical
Minor formatting cleanup
Added creation of include/ folder in bamtools root directory at build time.
Fixed: Improper sorting -byname
Moved BuildCharData() from BamReader to BamAlignment
Added static library to build step.
Implemented proper -byname sorting (finally).
Updated to 0.9.1
Added SAM header-handling classes for read/write/validate.
Added explicit copy ctors to SamHeader data structures
Update to BamTools API 0.9.2 with exposure of SamHeader object from BamReader and to BamWriter
Removed explicit keyword from SamHeader-related object copy ctors
Added BamConstants.h
Minor update to API version 0.9.3 - addition of SamHeader::SetHeaderText().
Minor formatting cleanup
Added UNSORTED to BamMultiReader::SortOrder types. Unsorted BAMs are 'merged' through a simple reader queue.
Removed SamHeaderValidatorPrivate pimpl. No real need for it since not exposed to API, and harder to test
Added ExportHeader command for BamConstants.h
Missed bug fix in BamMultiMerger in early commit. Fixed now.
Bug fix in SamHeaderVersion::SetVersion()
Attempt to fix SamHeaderVersion compile bug
Major update to BamTools version 1.0
Updated Doxyfile, attempt to fix online file access
Major performance boost to startup & random-access - especially for the
Rolled back the BGZF buffer size to the original 64K. 256K was causing
Brought API up to compliance with recent SAM Format Spec (v1.4-r962)
Modified BamAlignment in attempt to resolve symbol issues on 64-bit systems.
Additional attempt to force -fPIC on CentOS
Fixed regression bug in index formats. Wasn't properly handling empty references
Removed debug statements that snuck into last commit
Fixed minimum offset error in BAI jumping
Minor cleanup to toolkit code formatting.
Added new ResolveTool - for paired-end resolution. Similar to functionality provided inthe deprecated (or soon to be) MosaikSort tool
Cleaned up help formatting & added some string utilities
Created 3 modes for ResolveTool: makeStats, markPairs, & twoPass
ConvertTool fix: removed extra space in (BAM->FASTA) header lines
Fixed some signed/unsigned InsertSize bugs in ResolveTool
Further fixes for ISIZE-handling in ResolveTool
Implemented better coupling of unmapped reads with mates during sorting
Added re-calculation of BamAlignment's BinID during
Removed pessimistic warnings when jumping to regions with no data, using
Fixed -fPIC issue for CentOS users.
Added unique-alignment checks for ResolveTool
Added a -minMQ (minimum map quality) option to ResolveTool
Implemented binary search through bins in BAI
Added "isSingleton" property to filter tool
Added support for "-" as indicator for stdin/stdout
Added empty IBamIODevice.h
Basic internal implementation of BamFile & BamPipe
Merge branches 'master' and 'iodevice' into iodevice
Refactored shared pipe/file behavior into ILocalIODevice
Removed 'core mode' concept from BamMultiReader internals
Removed unnecessary peek-and-rewind behavior in BamMultiReader
Minor cleanup
Merge branches 'master' and 'iodevice' into iodevice
Fixed typo in error messages
Fix: unmapped reads now pushed to end of coordinate-sorted BAM
Initial test run of new BamAlgorithms
MultiReader (&MultiMerger) now using Algorithms::Sort objects
merge conflict
Removed duplicated method that snuck past a prior merge conflict resolution
First stab at templated tag access in BamAlignment
Removed STDERR pollution by API
Merge with earlier IODevice work
Cleaned up output/exception/asserts, etc after last merge
Converted intervals from 0-based, CLOSED to 0-based, HALF-OPEN
Updated Doxygen comments
Cleaned up intra-API includes & moved version numbers to 2.0.0
Removed index cache mode
Updated Doxyfile to reflect version 2.0.0
Cleanup missed by earlier "includes cleanup" commit
Fixed typo
Bug fix in BgzfStream I/O
Cleanup in SortTool
Major speedup in SamSequenceDictionary & SamReadGroupDictionary classes
Added GetSoftClips() method to BamAlignment
Minor cleanup in FilterTool
Regression fixed: wasn't properly merging from multiple BAMs
Fixed regression: improper @SQ line ordering in SamHeader output
Removed data duplication in last update to Sam*Dictionaries
Regression fixed: error in BamAlignment tag access methods
Removed some debugging 'error string' messages that snuck into last
Organized api/internal into subdirs
Implemented basic TCP support layer
Added FTP support (text-tested, not BAM)
Added generic I/O device to BamIndex side of things
Updated file headers (filename, license, description, etc)
Removed spurious assert
Basic Windows implementation
Initial test suite commit
Updated CMakeLists.txt files
merge with remoteio branch
Post-merge cleanup
Reorganized test suite source tree
Fixed EOF issues on *nix platforms
Rolled back test suite code from master until it's ready for full merge
Fixed: premature EOF issues & updated Windows implementation
Fixed: split tool crash when trying to split unmapped reads by reference
Added support for custom reference prefix in split tool
Nonstandard, user-defined tags now allowed in SAM header text
Fixed: bad_alloc in socket buffer on some machines
Removed use of std::map::at() in HttpHeader, not a standard STL method
Fixed: const-related typo in last commit
Fixed regression: missing EOF empty block on BgzfStream::Close()
Fixed: error in BamWriter metadata output on big-endian systems
Provided initialization values for previously unspecified (potentially
PileupEngine bugfix
PileupEngine performance improvement for high coverage
FASTA reader - performance improvement for single-base fetching
Fixed: sorting order lost during merge step of sort tool, if input BAM
Fixed: invalidated by-name sort order in some cases
Added proper handling for empty or ignored ("*") alignment fields:
Merge branch 'master' of github.com:pezmaster31/bamtools
Brought Doxyfile's version number up to date
Bug fix: error in index file creation when sorted BAM has empty
Fixed: improper mode check in local I/O device
Fixed: convert tool - improper unsigned char handling in tags
gabeiscoding (2):
Bug discovered. The chunkStop was not being read from the correct offset (rather always being read as the first chunkStart value for the # alignment chunks in that bin of the index.
In standard indexed BAM files with with sparce coverage (our test case was a roughly 1M read RNAseq BAM file), queries made to intervals may not have any of the candidate offesets present in the index as the BAM index only contains bins that have reads.
mikaels (12):
Initial import.
Added BamConversion to the make clean command
Defined some of the non-standard data types for compatibility with Visual Studio.
Updated the header text to give credit to the Broad Institute for the bgzf routines.
Made many improvements to the code that pass the stricter syntax checking in Visual Studio.
Removed the profiling options since they shouldn't be standard.
removed DOS line endings
Added support for the tag data and provided a GetReadGroup accessor.
Added tag data support.
Forgot some include statements.
Fixed some of the output for tag data.
fixed a bug where the terminal null wasn't being saved in SaveAlignment.
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