[med-svn] [SCM] bamtools annotated tag, upstream/2.2, created. upstream/2.2

Michael R. Crusoe michael.crusoe at gmail.com
Thu Nov 8 03:12:02 UTC 2012


The annotated tag, upstream/2.2 has been created
        at  922fbf67e058dc95f89381eb2ed652a0bdff828b (tag)
   tagging  9ed24dd6b91d8abac59af1cecda064fbf2da27bf (commit)
 tagged by  Michael R. Crusoe
        on  Wed Nov 7 14:11:06 2012 -0700

- Shortlog ------------------------------------------------------------
Upstream version 2.2

Alec Chapman (1):
      Fix Visual Studio compiler errors.

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.

Michael R. Crusoe (1):
      Imported Upstream version 2.2

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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