bamtools.git
5 years agoClarified documentation on BamReader::GetNextAlignmentCore master
Derek Barnett [Mon, 29 Jul 2013 21:14:01 +0000 (17:14 -0400)]
Clarified documentation on BamReader::GetNextAlignmentCore

5 years agoUpdated BamAlignment documentation, re: QueryBases field (issue #12)
Derek Barnett [Thu, 25 Jul 2013 18:22:50 +0000 (14:22 -0400)]
Updated BamAlignment documentation, re: QueryBases field (issue #12)

5 years agoMinor version bump - 2.3.0
Derek Barnett [Wed, 24 Jul 2013 20:24:28 +0000 (16:24 -0400)]
Minor version bump - 2.3.0
  * stabilized remote file support
  * additional bug fixes & feature requests
  * bamtools-utils & jsoncpp libs now built as static libs by default
(issue #55)

5 years agoStablized HTTP access on all platforms. (issue #54, issue #11)
Derek Barnett [Wed, 24 Jul 2013 20:08:13 +0000 (16:08 -0400)]
Stablized HTTP access on all platforms. (issue #54, issue #11)

5 years agoMerge branch 'master' of https://github.com/pezmaster31/bamtools
Derek Barnett [Wed, 24 Jul 2013 20:00:39 +0000 (16:00 -0400)]
Merge branch 'master' of https://github.com/pezmaster31/bamtools

5 years agoMerge pull request #81 from chmille4/master
Derek Barnett [Wed, 24 Jul 2013 19:59:22 +0000 (12:59 -0700)]
Merge pull request #81 from chmille4/master

Fix invalid json output

5 years agoMerge pull request #72 from grenaud/master
Derek Barnett [Wed, 24 Jul 2013 19:57:59 +0000 (12:57 -0700)]
Merge pull request #72 from grenaud/master

fixed copy of SamHeader.cpp

5 years agoAdded model description to stats file header in 'bamtools resolve' tool.
Derek Barnett [Wed, 24 Jul 2013 19:56:40 +0000 (15:56 -0400)]
Added model description to stats file header in 'bamtools resolve' tool.
(issue #76)

5 years agoAdded '-tagPrefix' option to 'bamtools split' tool. (issue #75)
Derek Barnett [Wed, 24 Jul 2013 19:30:03 +0000 (15:30 -0400)]
Added '-tagPrefix' option to 'bamtools split' tool. (issue #75)

5 years agoAdded new '-seed' parameter to 'bamtools random' tool. (issue #73)
Derek Barnett [Wed, 24 Jul 2013 19:02:33 +0000 (15:02 -0400)]
Added new '-seed' parameter to 'bamtools random' tool. (issue #73)

5 years agoRelated to last commit - fixed another instance of '_WIN32'
Derek Barnett [Wed, 24 Jul 2013 18:50:30 +0000 (14:50 -0400)]
Related to last commit - fixed another instance of '_WIN32'

5 years agoChanged platform check to use standard cmake variable (issue #66)
Derek Barnett [Wed, 24 Jul 2013 18:48:09 +0000 (14:48 -0400)]
Changed platform check to use standard cmake variable (issue #66)
  - 'WIN32' instead of '_WIN32'

5 years agoFixed: bamtools coverage not flushing at end (issue #64)
Derek Barnett [Wed, 24 Jul 2013 18:37:50 +0000 (14:37 -0400)]
Fixed: bamtools coverage not flushing at end (issue #64)

5 years agoFix invalid json output
Chase Miller [Wed, 24 Jul 2013 17:02:09 +0000 (13:02 -0400)]
Fix invalid json output

add quotes to the filename variable so that the json outputed is valid json

5 years agoAdded length property to filter tool.
Derek Barnett [Fri, 3 May 2013 21:29:53 +0000 (17:29 -0400)]
Added length property to filter tool.
 * Queries against the BamAlignment::Length field.

5 years agoFixed: error in FilterTool - mishandling of ASCII tag values
Derek Barnett [Sun, 28 Apr 2013 02:51:32 +0000 (22:51 -0400)]
Fixed: error in FilterTool - mishandling of ASCII tag values

6 years agoFixed SamHeader copy
grenaud [Tue, 12 Feb 2013 17:59:53 +0000 (18:59 +0100)]
Fixed SamHeader copy

6 years agoFixed: bug where first alignments were dropped after setting explicit merge order
Derek Barnett [Tue, 15 Jan 2013 02:08:01 +0000 (21:08 -0500)]
Fixed: bug where first alignments were dropped after setting explicit merge order

6 years agoUpdated MergeOrder enum documentation
Derek Barnett [Tue, 15 Jan 2013 01:41:23 +0000 (20:41 -0500)]
Updated MergeOrder enum documentation

6 years agoFixed version number
Derek Barnett [Tue, 15 Jan 2013 01:36:24 +0000 (20:36 -0500)]
Fixed version number

6 years agoAdded explicit merge order to BamMultiReader
Derek Barnett [Tue, 15 Jan 2013 01:31:23 +0000 (20:31 -0500)]
Added explicit merge order to BamMultiReader

6 years agoAdded the "-list" option to all toolkit utilities that accept multiple
Derek Barnett [Mon, 10 Dec 2012 18:23:10 +0000 (13:23 -0500)]
Added the "-list" option to all toolkit utilities that accept multiple
BAM files as input (issue #67)

6 years agoMerge pull request #67 from ekg/master
Derek Barnett [Mon, 10 Dec 2012 17:03:02 +0000 (09:03 -0800)]
Merge pull request #67 from ekg/master

Add input file list method to bamtools merge

6 years agoFixed: BamWriter - quality string starting with '*' (GH issue #68)
Derek Barnett [Mon, 10 Dec 2012 16:59:56 +0000 (11:59 -0500)]
Fixed: BamWriter - quality string starting with '*' (GH issue #68)

6 years agoresolve bamtools #68
Erik Garrison [Fri, 7 Dec 2012 23:07:55 +0000 (18:07 -0500)]
resolve bamtools #68

Check that the quality string is fully comprised of "*", rather than if
the first character is "*".

6 years agoMerge branch 'master' of git://github.com/pezmaster31/bamtools
Erik Garrison [Fri, 7 Dec 2012 22:30:06 +0000 (17:30 -0500)]
Merge branch 'master' of git://github.com/pezmaster31/bamtools

6 years agoVersion 2.2.2
Derek Barnett [Tue, 4 Dec 2012 16:42:50 +0000 (11:42 -0500)]
Version 2.2.2
  * Added: BamAlignment::GetArrayTagType()

6 years agoadd input file list method to bamtools merge
Erik Garrison [Thu, 29 Nov 2012 17:34:46 +0000 (12:34 -0500)]
add input file list method to bamtools merge

By using -list users can specify a file list.  Workaround for the case
when there are more input files than allowed by the maximum number of
command-line arguments.

6 years agoFixed: typo in BamReader.h
Derek Barnett [Mon, 19 Nov 2012 17:51:48 +0000 (12:51 -0500)]
Fixed: typo in BamReader.h

6 years agoVersion 2.2.1
Derek Barnett [Mon, 19 Nov 2012 17:24:55 +0000 (12:24 -0500)]
Version 2.2.1
 * Added:
     BamAlignment::GetTagNames()
     BamReader::GetConstSamHeader()
 * Fixed:
     'bamtools convert' - issues with unsigned char data in tags
     empty quality string handling in BamWriter

6 years agoFixed: BamWriter behavior on missing quality string (0xFF)
Derek Barnett [Mon, 19 Nov 2012 04:55:53 +0000 (23:55 -0500)]
Fixed: BamWriter behavior on missing quality string (0xFF)
 * See Issue #65

6 years agoAdded GetConstSamHeader() to BamReader
Derek Barnett [Mon, 19 Nov 2012 04:48:59 +0000 (23:48 -0500)]
Added GetConstSamHeader() to BamReader
 * Allows for more efficient (read-only) access to SamHeader data

6 years agoAdded GetTagNames method to BamAlignment
Derek Barnett [Mon, 19 Nov 2012 04:23:13 +0000 (23:23 -0500)]
Added GetTagNames method to BamAlignment

6 years agoFixed: regression in convert tool - SAM tags contained unreadable chars for int8...
Derek Barnett [Mon, 12 Nov 2012 04:11:57 +0000 (23:11 -0500)]
Fixed: regression in convert tool - SAM tags contained unreadable chars for int8/uint8 types

6 years agoMerge branch 'master' of https://github.com/pezmaster31/bamtools
Derek Barnett [Thu, 18 Oct 2012 16:28:01 +0000 (12:28 -0400)]
Merge branch 'master' of https://github.com/pezmaster31/bamtools

6 years agoVersion 2.2
Derek Barnett [Thu, 18 Oct 2012 16:24:20 +0000 (12:24 -0400)]
Version 2.2
 * Added support for running in NodeJS (fixed: piping issues)

6 years agoFixed: convert tool - improper unsigned char handling in tags
derek [Tue, 25 Sep 2012 17:02:54 +0000 (13:02 -0400)]
Fixed: convert tool - improper unsigned char handling in tags

6 years agoFixed: improper mode check in local I/O device
derek [Fri, 27 Jul 2012 14:44:51 +0000 (10:44 -0400)]
Fixed: improper mode check in local I/O device

6 years agoBug fix: error in index file creation when sorted BAM has empty
derek [Sat, 26 May 2012 01:43:32 +0000 (21:43 -0400)]
Bug fix: error in index file creation when sorted BAM has empty
references at end of file, followed by unaligned reads

6 years agoBrought Doxyfile's version number up to date
derek [Wed, 4 Apr 2012 22:34:50 +0000 (18:34 -0400)]
Brought Doxyfile's version number up to date

6 years agoMerge branch 'master' of github.com:pezmaster31/bamtools
derek [Wed, 4 Apr 2012 22:29:17 +0000 (18:29 -0400)]
Merge branch 'master' of github.com:pezmaster31/bamtools

6 years agoAdded proper handling for empty or ignored ("*") alignment fields:
derek [Wed, 4 Apr 2012 22:28:23 +0000 (18:28 -0400)]
Added proper handling for empty or ignored ("*") alignment fields:
QueryBases & Qualities

6 years agoMerge pull request #41 from tobiasmarschall/master
Derek Barnett [Wed, 4 Apr 2012 18:47:01 +0000 (11:47 -0700)]
Merge pull request #41 from tobiasmarschall/master

Include header sys/filio.h when compiling on SunOS.

6 years agoFixed: invalidated by-name sort order in some cases
derek [Wed, 4 Apr 2012 17:17:21 +0000 (13:17 -0400)]
Fixed: invalidated by-name sort order in some cases
 * due to (unintentional) member variable stored as reference

6 years agoInclude header sys/filio.h for SunOS. Otherwise TcpSocketEngine_unix_p.cpp does not...
Tobias Marschall [Tue, 27 Mar 2012 16:28:02 +0000 (18:28 +0200)]
Include header sys/filio.h for SunOS. Otherwise TcpSocketEngine_unix_p.cpp does not compile because FIONREAD is not found.

6 years agoFixed: sorting order lost during merge step of sort tool, if input BAM
derek [Tue, 27 Mar 2012 16:03:54 +0000 (12:03 -0400)]
Fixed: sorting order lost during merge step of sort tool, if input BAM
lacked SAM header
 * Due to lack of SO tag in temp files. This tag is set just fine on
input BAMs containing SAM headers. However, when an input file lacked
one, especially the (required) VN number, the entire @HD line was
dropped.
 * Forcing the current SAM version number, if none exists, on sort
output.

6 years agoMerge pull request #40 from tobiasmarschall/master
Derek Barnett [Mon, 26 Mar 2012 18:30:14 +0000 (11:30 -0700)]
Merge pull request #40 from tobiasmarschall/master

Fixed: uninitialized buffer in BamReaderPrivate::LoadNextAlignment

6 years agoMerge pull request #39 from leecbaker/master
Derek Barnett [Mon, 26 Mar 2012 18:05:12 +0000 (11:05 -0700)]
Merge pull request #39 from leecbaker/master

Fixed: comments are lost from header when copying a SamHeader

6 years agoFix uninitialized buffer in BamReaderPrivate::LoadNextAlignment
Tobias Marschall [Fri, 23 Mar 2012 10:04:33 +0000 (11:04 +0100)]
Fix uninitialized buffer in BamReaderPrivate::LoadNextAlignment

6 years agoFix: Comment lines in header get lost when copying a SamHeader object.
Lee Baker [Sun, 18 Mar 2012 07:00:47 +0000 (20:00 +1300)]
Fix: Comment lines in header get lost when copying a SamHeader object.

6 years agoFASTA reader - performance improvement for single-base fetching
derek [Fri, 9 Mar 2012 05:34:14 +0000 (00:34 -0500)]
FASTA reader - performance improvement for single-base fetching

6 years agoPileupEngine performance improvement for high coverage
derek [Fri, 9 Mar 2012 05:27:41 +0000 (00:27 -0500)]
PileupEngine performance improvement for high coverage

6 years agoPileupEngine bugfix
derek [Fri, 9 Mar 2012 05:05:24 +0000 (00:05 -0500)]
PileupEngine bugfix

7 years agoProvided initialization values for previously unspecified (potentially
derek [Thu, 23 Feb 2012 02:49:18 +0000 (21:49 -0500)]
Provided initialization values for previously unspecified (potentially
garbage) integer fields in default-constructed BamAlignments

7 years agoFixed: error in BamWriter metadata output on big-endian systems
derek [Mon, 13 Feb 2012 17:16:38 +0000 (12:16 -0500)]
Fixed: error in BamWriter metadata output on big-endian systems

7 years agoFixed regression: missing EOF empty block on BgzfStream::Close()
derek [Tue, 17 Jan 2012 16:47:13 +0000 (11:47 -0500)]
Fixed regression: missing EOF empty block on BgzfStream::Close()

7 years agoFixed: const-related typo in last commit
derek [Sat, 14 Jan 2012 03:43:45 +0000 (22:43 -0500)]
Fixed: const-related typo in last commit

7 years agoRemoved use of std::map::at() in HttpHeader, not a standard STL method
derek [Fri, 13 Jan 2012 17:06:22 +0000 (12:06 -0500)]
Removed use of std::map::at() in HttpHeader, not a standard STL method

7 years agoFixed: bad_alloc in socket buffer on some machines
derek [Thu, 5 Jan 2012 19:55:19 +0000 (14:55 -0500)]
Fixed: bad_alloc in socket buffer on some machines

7 years agoNonstandard, user-defined tags now allowed in SAM header text
derek [Thu, 8 Dec 2011 08:26:16 +0000 (03:26 -0500)]
Nonstandard, user-defined tags now allowed in SAM header text

7 years agoAdded support for custom reference prefix in split tool
derek [Thu, 8 Dec 2011 08:24:31 +0000 (03:24 -0500)]
Added support for custom reference prefix in split tool

7 years agoFixed: split tool crash when trying to split unmapped reads by reference
derek [Thu, 8 Dec 2011 08:14:17 +0000 (03:14 -0500)]
Fixed: split tool crash when trying to split unmapped reads by reference

7 years agoFixed: premature EOF issues & updated Windows implementation
derek [Thu, 8 Dec 2011 07:59:37 +0000 (02:59 -0500)]
Fixed: premature EOF issues & updated Windows implementation

7 years agoRolled back test suite code from master until it's ready for full merge
derek [Thu, 8 Dec 2011 05:35:02 +0000 (00:35 -0500)]
Rolled back test suite code from master until it's ready for full merge

7 years agoFixed EOF issues on *nix platforms
derek [Thu, 8 Dec 2011 05:26:10 +0000 (00:26 -0500)]
Fixed EOF issues on *nix platforms

7 years agoReorganized test suite source tree
derek [Tue, 29 Nov 2011 02:59:09 +0000 (21:59 -0500)]
Reorganized test suite source tree

7 years agoPost-merge cleanup
derek [Tue, 29 Nov 2011 00:09:58 +0000 (19:09 -0500)]
Post-merge cleanup

7 years agomerge with remoteio branch
derek [Mon, 28 Nov 2011 23:55:31 +0000 (18:55 -0500)]
merge with remoteio branch

7 years agoUpdated CMakeLists.txt files
derek [Mon, 28 Nov 2011 23:48:59 +0000 (18:48 -0500)]
Updated CMakeLists.txt files

7 years agoInitial test suite commit
derek [Mon, 28 Nov 2011 23:48:12 +0000 (18:48 -0500)]
Initial test suite commit

7 years agoBasic Windows implementation
derek [Thu, 17 Nov 2011 02:02:26 +0000 (21:02 -0500)]
Basic Windows implementation

7 years agoRemoved spurious assert
derek [Tue, 15 Nov 2011 03:20:54 +0000 (22:20 -0500)]
Removed spurious assert

7 years agoUpdated file headers (filename, license, description, etc)
derek [Thu, 10 Nov 2011 18:39:14 +0000 (13:39 -0500)]
Updated file headers (filename, license, description, etc)

7 years agoAdded generic I/O device to BamIndex side of things
derek [Thu, 10 Nov 2011 04:58:20 +0000 (23:58 -0500)]
Added generic I/O device to BamIndex side of things
 * Remote BAM access (now w/ random access) seems to be working with the
simple test cases so far
 * Major TODO: not yet implemented for Windows

7 years agoAdded FTP support (text-tested, not BAM)
derek [Wed, 9 Nov 2011 22:34:48 +0000 (17:34 -0500)]
Added FTP support (text-tested, not BAM)

7 years agoImplemented basic TCP support layer
derek [Mon, 7 Nov 2011 17:50:10 +0000 (12:50 -0500)]
Implemented basic TCP support layer
 * buffered I/O
 * design should support future expansion of protocols, proxies, etc
 * so far, HTTP range requests working well (on plain HTML text tests,
not yet BAM-tested)

7 years agoOrganized api/internal into subdirs
derek [Tue, 25 Oct 2011 16:33:54 +0000 (12:33 -0400)]
Organized api/internal into subdirs

7 years agoRemoved some debugging 'error string' messages that snuck into last
derek [Mon, 17 Oct 2011 19:55:12 +0000 (15:55 -0400)]
Removed some debugging 'error string' messages that snuck into last
commit

7 years agoRegression fixed: error in BamAlignment tag access methods
derek [Mon, 17 Oct 2011 03:30:34 +0000 (23:30 -0400)]
Regression fixed: error in BamAlignment tag access methods

7 years agoRemoved data duplication in last update to Sam*Dictionaries
derek [Sun, 16 Oct 2011 05:48:00 +0000 (01:48 -0400)]
Removed data duplication in last update to Sam*Dictionaries

7 years agoFixed regression: improper @SQ line ordering in SamHeader output
derek [Fri, 14 Oct 2011 16:42:15 +0000 (12:42 -0400)]
Fixed regression: improper @SQ line ordering in SamHeader output

7 years agoRegression fixed: wasn't properly merging from multiple BAMs
derek [Fri, 14 Oct 2011 05:14:30 +0000 (01:14 -0400)]
Regression fixed: wasn't properly merging from multiple BAMs

7 years agoMinor cleanup in FilterTool
derek [Fri, 14 Oct 2011 05:13:30 +0000 (01:13 -0400)]
Minor cleanup in FilterTool

7 years agoAdded GetSoftClips() method to BamAlignment
derek [Thu, 13 Oct 2011 14:03:22 +0000 (10:03 -0400)]
Added GetSoftClips() method to BamAlignment

7 years agoMajor speedup in SamSequenceDictionary & SamReadGroupDictionary classes
derek [Wed, 12 Oct 2011 20:30:59 +0000 (16:30 -0400)]
Major speedup in SamSequenceDictionary & SamReadGroupDictionary classes
 * Please note that this does introduce a minor source-incompatibility,
only affecting those working directly with the provided Sam*Iterator
typedefs. The short answer is that the iterator now references a
std::pair instead of the 'plain old' data. Use the pair's "second" field
to access the desired SamSequence or SamReadGroup.
 * Doxygen docs have been updated to reflect this and provide a bit more
explanation/examples (in docs folder run 'doxygen Doxyfile' to get the
updated API pages).

7 years agoCleanup in SortTool
derek [Tue, 11 Oct 2011 20:52:51 +0000 (16:52 -0400)]
Cleanup in SortTool
 * Now using the new BamTools::Algorithms::Sort function objects
 * Special handling of unmapped alignments should no longer be necessary
as the sorting function objects (also used by multi-reader merging
strategy) handles those cases.

7 years agoBug fix in BgzfStream I/O
derek [Tue, 11 Oct 2011 19:21:58 +0000 (15:21 -0400)]
Bug fix in BgzfStream I/O

7 years agoFixed typo
derek [Tue, 11 Oct 2011 17:34:13 +0000 (13:34 -0400)]
Fixed typo

7 years agoCleanup missed by earlier "includes cleanup" commit
derek [Tue, 11 Oct 2011 12:35:36 +0000 (08:35 -0400)]
Cleanup missed by earlier "includes cleanup" commit

7 years agoUpdated Doxyfile to reflect version 2.0.0
derek [Tue, 11 Oct 2011 05:09:35 +0000 (01:09 -0400)]
Updated Doxyfile to reflect version 2.0.0

7 years agoRemoved index cache mode
derek [Tue, 11 Oct 2011 04:04:54 +0000 (00:04 -0400)]
Removed index cache mode

7 years agoCleaned up intra-API includes & moved version numbers to 2.0.0
derek [Mon, 10 Oct 2011 22:29:53 +0000 (18:29 -0400)]
Cleaned up intra-API includes & moved version numbers to 2.0.0

7 years agoUpdated Doxygen comments
derek [Mon, 10 Oct 2011 21:26:46 +0000 (17:26 -0400)]
Updated Doxygen comments

7 years agoConverted intervals from 0-based, CLOSED to 0-based, HALF-OPEN
derek [Sun, 9 Oct 2011 03:47:07 +0000 (23:47 -0400)]
Converted intervals from 0-based, CLOSED to 0-based, HALF-OPEN

7 years agoCleaned up output/exception/asserts, etc after last merge
derek [Fri, 7 Oct 2011 22:19:09 +0000 (18:19 -0400)]
Cleaned up output/exception/asserts, etc after last merge

7 years agoMerge with earlier IODevice work
derek [Fri, 7 Oct 2011 20:11:43 +0000 (16:11 -0400)]
Merge with earlier IODevice work
 * This commit still has some console pollution. I need to work in the
recent Exception/ErrorString approach, but wanted to go ahead and do the
merge-conflict resolution now before diving into remote file support.

7 years agoRemoved STDERR pollution by API
derek [Fri, 7 Oct 2011 19:12:57 +0000 (15:12 -0400)]
Removed STDERR pollution by API
  * Accomplished this by introducing a GetErrorString() on most API
objects. When a method returns false, you can ignore it, parse the error
string to decide what to do next, prompt the user, make a sandwich,
whatever. But nothing should leak out to the console.
 * Internally the error messages are passed by a new BamException class.
This new exception should not cross the library boundary. The exception
should be caught "under the hood" and its what() string should be
(possibly formatted and) stored as the error string in one of the high-

7 years agoFirst stab at templated tag access in BamAlignment
derek [Tue, 4 Oct 2011 04:44:22 +0000 (00:44 -0400)]
First stab at templated tag access in BamAlignment
 * Seems to work OK, but will definitely need further testing to be sure

7 years agoRemoved duplicated method that snuck past a prior merge conflict resolution
derek [Tue, 4 Oct 2011 04:39:40 +0000 (00:39 -0400)]
Removed duplicated method that snuck past a prior merge conflict resolution

7 years agomerge conflict
derek [Mon, 3 Oct 2011 20:50:56 +0000 (16:50 -0400)]
merge conflict