[med-svn] [SCM] bamtools branch, master, created. 78243dc0bb2c4f8b29ec198d160b888911c2888c
Michael R. Crusoe
michael.crusoe at gmail.com
Wed Nov 7 21:49:20 UTC 2012
The branch, master has been created
at 78243dc0bb2c4f8b29ec198d160b888911c2888c (commit)
- Shortlog ------------------------------------------------------------
commit 78243dc0bb2c4f8b29ec198d160b888911c2888c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 13:26:44 2012 -0700
Revert "Fixed: convert tool - improper unsigned char handling in tags"
This reverts commit 9527e223ea52af559498ca2984e844c024ed6997.
commit 2f3b5a2171a469ef0877c793f7cd702bf998b64a
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 13:25:18 2012 -0700
Revert "Install libbamtools to $prefix/lib"
This reverts commit b39e8537886bb9996c8cfc8a344d95e4caffc052.
commit 51e00433e3ce9c5338ed3b6746c43dfa24fdb00e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 13:12:00 2012 -0700
merge
commit 506342e15566b5a01b2250fc8fc2cc6c8eeac30f
Merge: 6fc1efe 9012a1f
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 13:10:34 2012 -0700
merge
commit 6fc1efe51954adba660a880bf8211cf2f5d01b00
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 12:32:04 2012 -0700
Revert "Fixed: convert tool - improper unsigned char handling in tags"
This is a post-release change that accidently was included. We'll patch it ourselves for now
This reverts commit d6dbd5e905cbee75b926112b1db9910b10f302e6.
commit 2f86720f78091d68e92b8dce441689e2e812c521
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 12:27:39 2012 -0700
remove timestamps from patches
commit 4e04fc6ed6b925d153f8f955ea7be8a0aa77337e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 12:24:17 2012 -0700
refresh patches
commit 38b4828d0bd30a9704f14c5f4dbbb85706bf79eb
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 12:21:19 2012 -0700
debian/rule simplification via debian/clean, longer description
commit f5ef85d035ecd1f54249a26be3382a3c82f1195d
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Nov 7 12:21:08 2012 -0700
debian/rule simplification via debian/clean, longer description
commit 269f961b43f20c281c27426541aa19950e2238cc
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Nov 6 19:47:11 2012 -0700
Include remaining build-deps
commit 1ec5c7b526227934128a11f91d09e07e9604d3c4
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Nov 6 16:16:24 2012 -0700
incorporate final merge for 2.2
commit 33e4741e21699aca9ab86d747dee98c335248c76
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Nov 6 16:08:42 2012 -0700
Revert "Install libbamtools to $prefix/lib"
This reverts commit b39e8537886bb9996c8cfc8a344d95e4caffc052.
commit e2bf1322c3d3510af417ce2f3c7c7922ae0879b8
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Nov 6 14:28:11 2012 -0700
Initial Debianization
commit 3252c05be7fcc62b5a465ff72fb3e76c693d2883
Author: Shaun Jackman <sjackman at gmail.com>
Date: Fri Jun 15 13:35:52 2012 -0700
Install libbamtools to $prefix/lib
Installing libraries to $prefix/lib/bamtools requires setting
LD_LIBRARY_PATH or the executable's rpath. Installing libraries to
$prefix/lib is cleaner.
commit d6dbd5e905cbee75b926112b1db9910b10f302e6
Author: derek <derekwbarnett at gmail.com>
Date: Tue Sep 25 13:02:54 2012 -0400
Fixed: convert tool - improper unsigned char handling in tags
commit 9012a1fbc41b58743a3d7cbe13572cc52ebb6291
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Nov 6 14:28:11 2012 -0700
Initial Debianization
commit b39e8537886bb9996c8cfc8a344d95e4caffc052
Author: Shaun Jackman <sjackman at gmail.com>
Date: Fri Jun 15 13:35:52 2012 -0700
Install libbamtools to $prefix/lib
Installing libraries to $prefix/lib/bamtools requires setting
LD_LIBRARY_PATH or the executable's rpath. Installing libraries to
$prefix/lib is cleaner.
commit a4fdee2f966f69286c77d8913d87cbf7af6422ad
Merge: bafc03f 9527e22
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Thu Oct 18 12:28:01 2012 -0400
Merge branch 'master' of https://github.com/pezmaster31/bamtools
commit bafc03f4ed7ed9ff1b3fb24874dc8a4a6d58e605
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Thu Oct 18 12:24:20 2012 -0400
Version 2.2
* Added support for running in NodeJS (fixed: piping issues)
commit 9527e223ea52af559498ca2984e844c024ed6997
Author: derek <derekwbarnett at gmail.com>
Date: Tue Sep 25 13:02:54 2012 -0400
Fixed: convert tool - improper unsigned char handling in tags
commit e235c55e4a2c5d88d13c932206db90991fa093e0
Author: derek <derekwbarnett at gmail.com>
Date: Fri Jul 27 10:44:51 2012 -0400
Fixed: improper mode check in local I/O device
commit 6111130f6d7b1ae06ac25178f8dc5006f0754cfc
Author: derek <derekwbarnett at gmail.com>
Date: Fri May 25 21:43:32 2012 -0400
Bug fix: error in index file creation when sorted BAM has empty
references at end of file, followed by unaligned reads
commit 6708a21b48a6021b10a544ef4fecef5f1aa0dd1d
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 4 18:34:50 2012 -0400
Brought Doxyfile's version number up to date
commit e5ef6c3265472f0a798a11ced6d0095f7934f6b7
Merge: 6bb3f90 bf86ea8
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 4 18:29:17 2012 -0400
Merge branch 'master' of github.com:pezmaster31/bamtools
commit 6bb3f902d3f8087112afd4dbf8a783b73b40db8d
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 4 18:28:23 2012 -0400
Added proper handling for empty or ignored ("*") alignment fields:
QueryBases & Qualities
commit bf86ea8b7772ee3e4c5b411134fa883ab5dbf7bd
Merge: 76bb08a 4f5a8b7
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Wed Apr 4 11:47:01 2012 -0700
Merge pull request #41 from tobiasmarschall/master
Include header sys/filio.h when compiling on SunOS.
commit d9a14ac04a9da82f7d511f0fba9ae0bf4797614d
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 4 13:17:21 2012 -0400
Fixed: invalidated by-name sort order in some cases
* due to (unintentional) member variable stored as reference
commit 4f5a8b711402201a64c22453b61937c9eef9825f
Author: Tobias Marschall <T.Marschall at cwi.nl>
Date: Tue Mar 27 18:28:02 2012 +0200
Include header sys/filio.h for SunOS. Otherwise TcpSocketEngine_unix_p.cpp does not compile because FIONREAD is not found.
commit 76bb08a359f3974eee3e96327b965ccf7958ed1a
Author: derek <derekwbarnett at gmail.com>
Date: Tue Mar 27 12:03:54 2012 -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.
commit cd6566664db03680573d36ca7ae70a243724c8a8
Merge: 662b1d5 146f515
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Mon Mar 26 11:30:14 2012 -0700
Merge pull request #40 from tobiasmarschall/master
Fixed: uninitialized buffer in BamReaderPrivate::LoadNextAlignment
commit 662b1d5e618c41bb393fffb47eac3d21cd66b5d2
Merge: 7f8b301 d87a3d2
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Mon Mar 26 11:05:12 2012 -0700
Merge pull request #39 from leecbaker/master
Fixed: comments are lost from header when copying a SamHeader
commit 146f51585f77be8da168cba28ec5a352903004d6
Author: Tobias Marschall <T.Marschall at cwi.nl>
Date: Fri Mar 23 11:04:33 2012 +0100
Fix uninitialized buffer in BamReaderPrivate::LoadNextAlignment
commit d87a3d2b453e3f4b6c5acc376870ef46f86a0337
Author: Lee Baker <lee at leecbaker.com>
Date: Sun Mar 18 20:00:47 2012 +1300
Fix: Comment lines in header get lost when copying a SamHeader object.
commit 7f8b301e2f43d4d50a79f6184f1c132c9e33d324
Author: derek <derekwbarnett at gmail.com>
Date: Fri Mar 9 00:34:14 2012 -0500
FASTA reader - performance improvement for single-base fetching
commit 6925f97878e99f8844d038273257c419c0c767b6
Author: derek <derekwbarnett at gmail.com>
Date: Fri Mar 9 00:27:41 2012 -0500
PileupEngine performance improvement for high coverage
commit b75f271eefc6d076c8995060db8b3a6b040555d1
Author: derek <derekwbarnett at gmail.com>
Date: Fri Mar 9 00:05:24 2012 -0500
PileupEngine bugfix
commit cf5ad68fc395bd521bf24274479a630d0f0d2d2c
Author: derek <derekwbarnett at gmail.com>
Date: Wed Feb 22 21:49:18 2012 -0500
Provided initialization values for previously unspecified (potentially
garbage) integer fields in default-constructed BamAlignments
commit db80a3a8da82dcdbd460fd03f098a33f3c6b13e6
Author: derek <derekwbarnett at gmail.com>
Date: Mon Feb 13 12:16:38 2012 -0500
Fixed: error in BamWriter metadata output on big-endian systems
commit 8a5d6508d8fc52b25c9129037e44cc448bafebc7
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jan 17 11:47:13 2012 -0500
Fixed regression: missing EOF empty block on BgzfStream::Close()
commit 1dd0e1cb8a8557dfb463bf4323f121614cb6fcb2
Author: derek <derekwbarnett at gmail.com>
Date: Fri Jan 13 22:43:45 2012 -0500
Fixed: const-related typo in last commit
commit af44c70b7a7205f04a676459a05fdcd61fc0e060
Author: derek <derekwbarnett at gmail.com>
Date: Fri Jan 13 12:06:22 2012 -0500
Removed use of std::map::at() in HttpHeader, not a standard STL method
commit 35eb5aa1ef552f0baccd9fc8cab61f3a13fe2adc
Author: derek <derekwbarnett at gmail.com>
Date: Thu Jan 5 14:55:19 2012 -0500
Fixed: bad_alloc in socket buffer on some machines
commit 466bc501dbf526f85f5d3d2ddf627342261e4d2e
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 03:26:16 2011 -0500
Nonstandard, user-defined tags now allowed in SAM header text
commit e7d0ca0a024a13d405872be90f381ff397cdaeec
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 03:24:31 2011 -0500
Added support for custom reference prefix in split tool
commit 5eb631a840b7f24b308ecf6eea118d020cbcdff2
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 03:14:17 2011 -0500
Fixed: split tool crash when trying to split unmapped reads by reference
commit 61f4f02a6f27510e96de59dda110f6e5de3236ba
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 02:59:37 2011 -0500
Fixed: premature EOF issues & updated Windows implementation
commit 2421926e573603541ecb63b1d399a28b8c4b2a6c
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 00:35:02 2011 -0500
Rolled back test suite code from master until it's ready for full merge
commit 12002997e431049bfe0548340e14edb8f2638994
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 8 00:26:10 2011 -0500
Fixed EOF issues on *nix platforms
commit b43ea794d871bd7fb832cb5deb0eaf8d62b7e9a6
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 28 21:59:09 2011 -0500
Reorganized test suite source tree
commit 29c554c08c72d265bb2110f2fd9019125224b595
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 28 19:09:58 2011 -0500
Post-merge cleanup
commit 8077f86ef52bfb08c17430b797c737d217d41cf3
Merge: a50400c c9ded8b
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 28 18:55:31 2011 -0500
merge with remoteio branch
commit a50400c186a05160e1164bf544571b739ff6fac8
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 28 18:48:59 2011 -0500
Updated CMakeLists.txt files
commit d6a5fdafd5490a20285566695c4aef16a2d57107
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 28 18:48:12 2011 -0500
Initial test suite commit
commit c9ded8b7ecb6bf17425df053b9c2f6858a77848e
Author: derek <derekwbarnett at gmail.com>
Date: Wed Nov 16 21:02:26 2011 -0500
Basic Windows implementation
commit e1cf57332e54eedff4cf3547de5372bd2d611088
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 14 22:20:54 2011 -0500
Removed spurious assert
commit e4cb7afa9b8774b4db39db1c60607460676419d3
Author: derek <derekwbarnett at gmail.com>
Date: Thu Nov 10 13:39:14 2011 -0500
Updated file headers (filename, license, description, etc)
commit d619466092e2d1b2c89c346f69d863875fd8ff8d
Author: derek <derekwbarnett at gmail.com>
Date: Wed Nov 9 23:58:20 2011 -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
commit 8e8ed0f0d520fa4d240ab98bd7cc0b0933777fdb
Author: derek <derekwbarnett at gmail.com>
Date: Wed Nov 9 17:34:48 2011 -0500
Added FTP support (text-tested, not BAM)
commit aace28299671f066bf2135ef28652f24fa1d8d26
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 7 12:50:10 2011 -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)
commit 90432a3736392f98803a5e8787f3db0dc5bb44ad
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 25 12:33:54 2011 -0400
Organized api/internal into subdirs
commit 8b4c010999a8d0c482d84bbf17c98dc4bbae02b7
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 17 15:55:12 2011 -0400
Removed some debugging 'error string' messages that snuck into last
commit
commit c3a7c31347d42a926214e2508d713975d124e8c6
Author: derek <derekwbarnett at gmail.com>
Date: Sun Oct 16 23:30:34 2011 -0400
Regression fixed: error in BamAlignment tag access methods
commit f82b860f94f9bf107c21acacf9df5aab6cf8c3e7
Author: derek <derekwbarnett at gmail.com>
Date: Sun Oct 16 01:48:00 2011 -0400
Removed data duplication in last update to Sam*Dictionaries
commit af6a3d8491e485969d2df306e41cb9439dec4039
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 14 12:42:15 2011 -0400
Fixed regression: improper @SQ line ordering in SamHeader output
commit 6a75f0d886c44d98a6fba6513d2f3e9f158659ed
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 14 01:14:30 2011 -0400
Regression fixed: wasn't properly merging from multiple BAMs
commit b54179efa36f08168a7209fb622f161491d75ad6
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 14 01:13:30 2011 -0400
Minor cleanup in FilterTool
commit 1b1108713c795c05fc845ba6373efcf4166acf43
Author: derek <derekwbarnett at gmail.com>
Date: Thu Oct 13 10:03:22 2011 -0400
Added GetSoftClips() method to BamAlignment
commit 270452a6f0a98cb1e4260b5501fe780c9b1806c0
Author: derek <derekwbarnett at gmail.com>
Date: Wed Oct 12 16:30:59 2011 -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).
commit 15a173d229110e7fbac63774890853d78539fa1d
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 16:52:51 2011 -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.
commit a847098d20d1bb39a45123c6b886479c6a97001a
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 15:21:58 2011 -0400
Bug fix in BgzfStream I/O
commit c80f364f4fcca3e585cbaadbe89ad1c42326669c
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 13:34:13 2011 -0400
Fixed typo
commit 4106e787c888bb743fdd778e4f3a9d241cc895f5
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 08:35:36 2011 -0400
Cleanup missed by earlier "includes cleanup" commit
commit 816d51eda70837fe5ce01ffc9aee2cc83722443f
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 01:09:35 2011 -0400
Updated Doxyfile to reflect version 2.0.0
commit 19077d59154eeb244af96b1fd9658e535c24c1be
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 11 00:04:54 2011 -0400
Removed index cache mode
commit 9f1ce8c47aeadb6dc1320b52ee671c3341b97935
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 10 18:29:53 2011 -0400
Cleaned up intra-API includes & moved version numbers to 2.0.0
commit 25a2a1f6598b6452455da96c28a7f58fd9e7ed2d
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 10 17:26:46 2011 -0400
Updated Doxygen comments
commit d776d518237008a804656ff27e9f06707d032ae2
Author: derek <derekwbarnett at gmail.com>
Date: Sat Oct 8 23:47:07 2011 -0400
Converted intervals from 0-based, CLOSED to 0-based, HALF-OPEN
commit 2e1822c9ed231b25fd474117a01a1492d4209fa4
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 7 18:19:09 2011 -0400
Cleaned up output/exception/asserts, etc after last merge
commit 8a90b7aefffaf186053ef4da96c8663bf528274a
Merge: 2e049ed c1fc1c5
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 7 16:11:43 2011 -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.
commit 2e049ed7f28881bce09653e60f5aea54bfd7afbf
Author: derek <derekwbarnett at gmail.com>
Date: Fri Oct 7 15:12:57 2011 -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-
commit 11fabb69eb8c86635dd9498679b72bf78b3af3d1
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 4 00:44:22 2011 -0400
First stab at templated tag access in BamAlignment
* Seems to work OK, but will definitely need further testing to be sure
commit 810613e2506b2dd8e16312f9f73346599943922c
Author: derek <derekwbarnett at gmail.com>
Date: Tue Oct 4 00:39:40 2011 -0400
Removed duplicated method that snuck past a prior merge conflict resolution
commit 1a93ff03d7e40d97c32e6f5966045ceaeb2f038a
Merge: a194fa0 daf6497
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 3 16:50:56 2011 -0400
merge conflict
commit daf64972794dbbdae4bea6a0495578708c86363b
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 3 16:33:44 2011 -0400
MultiReader (&MultiMerger) now using Algorithms::Sort objects
commit 038f0e1dda24b2d6765cc8c878b7dbdc5f922ed6
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 30 16:20:28 2011 -0400
Initial test run of new BamAlgorithms
commit a194fa05d2c9000eec969861f9b92dd2a7d31095
Author: derek <derekwbarnett at gmail.com>
Date: Wed Sep 28 12:26:25 2011 -0400
Fix: unmapped reads now pushed to end of coordinate-sorted BAM
commit 55bd722399551caec548b6ca9a60151199118b88
Author: derek <derekwbarnett at gmail.com>
Date: Tue Sep 27 11:46:40 2011 -0400
Fixed typo in error messages
commit 08215752fee2e55fc6e0114030f1f8836d38aee0
Merge: 72f5b82 db63f7c
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Mon Sep 26 21:10:59 2011 -0700
Merge pull request #16 from gabeiscoding/patch-2
Fixed: Crash in BamStandardIndex::GetOffset for small BAM files
commit db63f7c21ac6e4dc1198a7cc211f2375788889fb
Author: gabeiscoding <gaberudy at gmail.com>
Date: Fri Sep 23 09:35:34 2011 -0600
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.
Without this bail out, we would get a crash. Returning false silently is the preferred behavior in our view as it allows our read logic to go to the next query and does not add noise to stderr.
commit c1fc1c5423ca73a1b5bcbe790650821d73e5959c
Merge: 57ff487 72f5b82
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 22:05:02 2011 -0400
Merge branches 'master' and 'iodevice' into iodevice
commit 72f5b82ad353b4cc9d6f8153f1ad19cc387b9597
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 21:40:06 2011 -0400
Minor cleanup
* Removed SourceForge URL from README
* Removed phrase "All rights reserved." from all files
commit 00cf2def91345c706120ab69056d3d41860ff5c5
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 18:49:44 2011 -0400
Removed unnecessary peek-and-rewind behavior in BamMultiReader
* Fixes some piping issues
commit c0da76176fbb6771e02d532246e5a464a957c382
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 18:32:44 2011 -0400
Removed 'core mode' concept from BamMultiReader internals
* Now char data is only generated if needed by multi-merger
implementation or on-demand by client call to
BamMultiReader::GetNextAlignment()
commit 57ff487e7acaf7f55a45c0a80cb9647bb1d83801
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 15:09:53 2011 -0400
Refactored shared pipe/file behavior into ILocalIODevice
commit 88577e25bbf4b6b43642cb679c5f9f5cba026fec
Merge: 243a21d 590fa35
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 12:07:31 2011 -0400
Merge branches 'master' and 'iodevice' into iodevice
commit 243a21d278e81d0a05997ad8bef109153443fb75
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 9 12:02:06 2011 -0400
Basic internal implementation of BamFile & BamPipe
* BgzfStream now working on IBamIODevice instead of FILE*
* BamReaderPrivate now queries stream's IsOpen() method instead of
touching member variable directly
* Empty implementations of BamHttp & BamFtp
* Added global BT_ASSERT_X macro for convenience
commit 590fa357b9b9a8dfdad2f8dc0c3c113c3b26fbfe
Merge: 86e9257 dd66486
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Thu Sep 8 13:59:09 2011 -0700
Merge pull request #15 from gabeiscoding/patch-1
Bug discovered. The chunkStop was not being read from the correct offset
commit dd6648692c398c783958be7e02fc669b16b5014a
Author: gabeiscoding <gaberudy at gmail.com>
Date: Thu Sep 8 07:32:48 2011 -0600
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.
The result of this is that chunkStop will never be >= minOffset (or maybe rarely, since it always equals the first chunkStart for the first chunk) and thus the linear index doesn't really help in reducing the number of seeks performed.
commit 1691db866bf895d6b2ad72f204ccb6bc9a35e7e3
Author: derek <derekwbarnett at gmail.com>
Date: Wed Sep 7 13:54:30 2011 -0400
Added empty IBamIODevice.h
commit 86e92576cd16354f09f6cbda6e6784d2d71d9399
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 2 13:01:43 2011 -0400
Added support for "-" as indicator for stdin/stdout
* Thanks to Aaron Quinlan for suggestion
commit 6a3fd9818d23876a2503a592fc6a806c6e6bc9bb
Author: derek <derekwbarnett at gmail.com>
Date: Fri Sep 2 12:35:54 2011 -0400
Added "isSingleton" property to filter tool
commit 971c4168ee75fd806dbc33b6adaf067b749fe14f
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jul 27 11:34:41 2011 -0400
Implemented binary search through bins in BAI
commit 12aca989c5389390ffe5c20a76c9be86ece393e2
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jul 6 12:24:00 2011 -0400
Added a -minMQ (minimum map quality) option to ResolveTool
commit 525fc971414d7f7b8b6022e741ebb275d3f68b6b
Merge: cbd3b76 1f79a22
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Tue Jun 28 09:37:30 2011 -0700
Merge pull request #13 from alecchap/master
Fixes for Visual Studio
commit cbd3b7633c78f91be456991e3ec751ed09ddf87e
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jun 28 12:31:25 2011 -0400
Added unique-alignment checks for ResolveTool
* Unique-ness determined by comparing MapQuality to 0
* Only pairs with both mates unique are used for the 'makeStats' median
fragment size calculation.
commit 1f79a2269614e11135ae5e6a35e70106dfe2a5d8
Author: Alec Chapman <achapman at alumni.princeton.edu>
Date: Mon Jun 27 21:58:30 2011 -0400
Fix Visual Studio compiler errors.
Don't use dynamic stack allocation (variable length arrays).
Rename bamtools target to bamtools_cmd to not conflict with BamTools target (they differ only in case).
bamtools_cmd only compiles if I remove bamtools_filter.cpp, which I haven't committed.
I also had to manually configure the include directory for zlib,
but that's probably due to having multiple copies floating around my machine.
commit 36187632f41f7f995580c35657ceaeaf2c47aa7a
Author: derek <derekwbarnett at gmail.com>
Date: Thu Jun 23 15:35:35 2011 -0400
Fixed -fPIC issue for CentOS users.
* Forced compiler flag that was not being automatically set by CMake on
that OS. Had previously set this on API library. Got feedback that it
worked there, so I added the flag to Utils & JsonCPP libs as well.
commit dc7614e9c8eb07be5d9ba80a67ce7cc2ac7e709e
Author: derek <derekwbarnett at gmail.com>
Date: Fri Jun 17 00:09:49 2011 -0400
Removed pessimistic warnings when jumping to regions with no data, using
the standard index format (not actually an error case, so no need to
alarm users with scary messages)
commit 3f1af3408a4b7cce7851c32be6f83a1ec366ec50
Author: derek <derekwbarnett at gmail.com>
Date: Thu Jun 16 22:13:26 2011 -0400
Added re-calculation of BamAlignment's BinID during
BamWriter::SaveAlignment() in all cases
* Previously, the bin IDs of purely "core-only" alignments were simply
written directly out to output BAM. However, in cases where alignment
Position is changed (re-alignment), the original bin ID may no longer be
correct.
commit 4dd0470141b23c771607cceb1e0b3e0e7cd51ca1
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jun 14 13:41:56 2011 -0400
Implemented better coupling of unmapped reads with mates during sorting
(assuming assigned same coordinates)
* Used std::stable_sort instead of std::sort, to preserve order
* Add checks at buffer boundary to keep mates from being split into
different temp files. This makes the buffer boundary "softer", but in
practice, shouldn't differ much if at all.
commit f3a8da2a83a6412f3f25269af09bdfb9b1014e02
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jun 14 13:16:36 2011 -0400
Further fixes for ISIZE-handling in ResolveTool
commit 59479653d9a0f96ecfe30b67d366a56d71a1973f
Author: derek <derekwbarnett at gmail.com>
Date: Mon Jun 13 15:37:36 2011 -0400
Fixed some signed/unsigned InsertSize bugs in ResolveTool
commit 4a2da65db87a3fd7db8f77d416c184a413b9f34f
Author: derek <derekwbarnett at gmail.com>
Date: Sat Jun 11 17:07:43 2011 -0400
ConvertTool fix: removed extra space in (BAM->FASTA) header lines
commit 1c3e9e8c0a913b28f370c7d07a1b520b308b9981
Author: derek <derekwbarnett at gmail.com>
Date: Sat Jun 11 17:05:43 2011 -0400
Created 3 modes for ResolveTool: makeStats, markPairs, & twoPass
* "TwoPass" mode (the initial implementation of the tool) effectively
eliminates piped BAMs as an input option, since you can't exactly rewind
stdin and start reading from the beginning.
* To get around this, I separated the two passes into separate "modes"
(-makeStats & -markPairs), that communicate via a simple, human-readable
stats summary file. Data can then be merged, filtered, etc and piped
into each mode if you don't mind the runtime of preprocessing twice but
don't want to physically store the unresolved intermediate BAM file.
commit ad3f59ce304c37faff88fbc5ea8c1df047326df4
Author: derek <derekwbarnett at gmail.com>
Date: Sat Jun 11 16:55:08 2011 -0400
Cleaned up help formatting & added some string utilities
commit 66ddb686203f754c010ca1538ebe69ba03f38f7f
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jun 7 15:47:42 2011 -0400
Added new ResolveTool - for paired-end resolution. Similar to functionality provided inthe deprecated (or soon to be) MosaikSort tool
commit a357e1a5853b5bd5a43ceb673269863afc54a08e
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jun 7 15:45:35 2011 -0400
Minor cleanup to toolkit code formatting.
commit 889210eae78b7e1a186b67aa0846c038f03906ab
Author: derek <derekwbarnett at gmail.com>
Date: Tue May 10 19:28:31 2011 -0400
Fixed minimum offset error in BAI jumping
commit f33f82336198d1608b713a90b89d010019a46c1a
Merge: b210d62 be36350
Author: Derek Barnett <derekwbarnett at gmail.com>
Date: Thu May 5 10:49:59 2011 -0700
Merge pull request #9 from bookest/patch-1
'make install' should install bin/bamtools
commit be3635006234e51a349bc8ab712850481b062afe
Author: Christopher Grim <christopher.grim at gmail.com>
Date: Thu May 5 10:17:59 2011 -0700
'make install' should install bin/bamtools
commit b210d62d64884731023e8b8a3af327b8627bdadc
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 27 02:22:30 2011 -0400
Removed debug statements that snuck into last commit
commit 497543a938d72b0218703c67b6fcf5bf756cf033
Author: derek <derekwbarnett at gmail.com>
Date: Wed Apr 27 02:19:15 2011 -0400
Fixed regression bug in index formats. Wasn't properly handling empty references
commit 79d621afbe6d4cf1a9b36a6167c1b4304b263ee0
Author: derek <derekwbarnett at gmail.com>
Date: Fri Apr 22 14:40:36 2011 -0400
Additional attempt to force -fPIC on CentOS
commit 2147eb1f35814c0c8f7f641bcccfb844c7a4fc35
Author: derek <derekwbarnett at gmail.com>
Date: Fri Apr 22 12:55:01 2011 -0400
Modified BamAlignment in attempt to resolve symbol issues on 64-bit systems.
commit cdf4bbcb19025398d429035fe672661a8c8d1a80
Author: derek <derekwbarnett at gmail.com>
Date: Tue Apr 19 19:01:01 2011 -0400
Brought API up to compliance with recent SAM Format Spec (v1.4-r962)
* Added support for new "binary array" tag type
* Added support for '=' and 'X' CIGAR ops
* Added support for multiple PG entries in header
* Added support for new RG fields
commit 9cf50963514decd5c272f52a0a019c6289d43c63
Author: derek <derekwbarnett at gmail.com>
Date: Tue Apr 5 13:37:01 2011 -0400
Rolled back the BGZF buffer size to the original 64K. 256K was causing
crashes on some systems.
commit a15dba1bdfe5a1a61e175cb18b1e2694cfcd1746
Author: derek <derekwbarnett at gmail.com>
Date: Tue Apr 5 12:43:31 2011 -0400
Major performance boost to startup & random-access - especially for the
use cases involving multiple (hundreds) of BAMs with BAI index files.
* This did require some changes to the BamIndex interface. I doubt man
y people are writing custom index format classes, but if you are one of
them and have any problems, feel free to contact me with questions.
commit 17f39f62875a7122ff09e3af647377e04afed563
Author: derek <derekwbarnett at gmail.com>
Date: Wed Mar 23 02:57:31 2011 -0400
Updated Doxyfile, attempt to fix online file access
commit 8c80d760637f8df39262683cd2570f0589423d36
Author: derek <derekwbarnett at gmail.com>
Date: Wed Mar 23 02:37:39 2011 -0400
Major update to BamTools version 1.0
commit 577b6032aa3d85616047c8aba6061dd8dad20cfc
Author: derek <derekwbarnett at gmail.com>
Date: Thu Feb 24 11:36:12 2011 -0500
Attempt to fix SamHeaderVersion compile bug
commit cbb397ffbd22976f39758eda399d69ab234c8184
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jan 19 12:57:13 2011 -0500
Bug fix in SamHeaderVersion::SetVersion()
commit 853ae3fc0acb9297bb1f0cf5bbc54d34a1af5a1a
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jan 19 12:08:52 2011 -0500
Missed bug fix in BamMultiMerger in early commit. Fixed now.
commit f63f2faca4e20277fcca2a6b4f8bc627f3dae2bd
Author: derek <derekwbarnett at gmail.com>
Date: Mon Jan 17 14:49:32 2011 -0500
Added ExportHeader command for BamConstants.h
commit 0b8c7955dc2fed672eab69b3319e70b9f3a0ac27
Author: derek <derekwbarnett at gmail.com>
Date: Mon Jan 17 14:45:09 2011 -0500
Removed SamHeaderValidatorPrivate pimpl. No real need for it since not exposed to API, and harder to test
commit 42444d414d2ab2e7831e4224c81165f2905f7096
Author: derek <derekwbarnett at gmail.com>
Date: Mon Jan 17 14:42:42 2011 -0500
Added UNSORTED to BamMultiReader::SortOrder types. Unsorted BAMs are 'merged' through a simple reader queue.
commit 4423944dcf9ab108ba012bceb5d5db4eb4cb561d
Author: derek <derekwbarnett at gmail.com>
Date: Thu Jan 13 01:40:25 2011 -0500
Minor formatting cleanup
commit 6f5c226a2892eca7e3446db18928ed0ce9f65daf
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jan 12 17:47:04 2011 -0500
Minor update to API version 0.9.3 - addition of SamHeader::SetHeaderText().
commit d51ee65181b527013be6e4087c1edc816505fbbb
Author: derek <derekwbarnett at gmail.com>
Date: Wed Jan 12 11:37:17 2011 -0500
Added BamConstants.h
commit 7e2b34b53dd34422b3f2308bda4bbe7ab3ee129d
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jan 11 22:43:51 2011 -0500
Removed explicit keyword from SamHeader-related object copy ctors
commit 90f57dc99f0af143f50a0afef447b50048a556f3
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jan 11 22:37:31 2011 -0500
Update to BamTools API 0.9.2 with exposure of SamHeader object from BamReader and to BamWriter
commit dc965ab6cd68e6e4b29544ae7340c571b0c7cf9f
Author: derek <derekwbarnett at gmail.com>
Date: Tue Jan 11 22:35:09 2011 -0500
Added explicit copy ctors to SamHeader data structures
commit ff5f2ec7c437660185a406d01739f42534105412
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 23 22:33:33 2010 -0500
Added SAM header-handling classes for read/write/validate.
* Not fully connected to the BamReader/Writer API yet, but will be
phased in soon.
* Will enable clients to query, modify & validate a BAM file's SAM
header data using the BamTools API, instead of having to use hand-rolled
string-parsing code on the result of BamReader::GetHeaderText().
commit e2a970e0f34f850692b9f94a96034f2165ebf1d6
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 23 21:26:02 2010 -0500
Updated to 0.9.1
* With changes to BamMultiReader interface.
commit 83255b02911cc3e267386e20bcb8747478b4c239
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 23 21:14:49 2010 -0500
Implemented proper -byname sorting (finally).
* BamMultiReader used to merge the "next" alignment based on (refID,
position). Extracted this and generalized to support merging on either
position OR alignment name.
commit 54cdbfab8659f13806645133196ce2df01b0ffb4
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 23 20:56:01 2010 -0500
Added static library to build step.
* Suggested & contributed by Rob Bradley.
commit 94193d06ce788ba7df8b7bd856a983d1e98daac6
Author: derek <derekwbarnett at gmail.com>
Date: Wed Dec 22 14:22:40 2010 -0500
Moved BuildCharData() from BamReader to BamAlignment
* This will enable even "lazier" population of the alignment character
data later in analysis, outside the context of reading it from the BAM
file
commit fffb4289693f599208e89cf73b4b22137ad7a26f
Author: derek <derekwbarnett at gmail.com>
Date: Thu Dec 16 12:33:32 2010 -0500
Fixed: Improper sorting -byname
commit 9747edd223402e4198dfb649d9b1ba6345549947
Author: derek <derekwbarnett at gmail.com>
Date: Wed Dec 15 15:39:54 2010 -0500
Added creation of include/ folder in bamtools root directory at build time.
* API-related headers are copied here to provide an explicit target for client code.
commit 81ffcac10d28190c191243226e3841d13746f89e
Author: derek <derekwbarnett at gmail.com>
Date: Mon Dec 13 15:53:12 2010 -0500
Minor formatting cleanup
commit 8cff313e03c7756e753c06097d710b8dc73b6eb7
Author: derek <derekwbarnett at gmail.com>
Date: Mon Dec 13 15:28:33 2010 -0500
Made BamAlignment flag queries symmetrical
* For example: there is now a SetIsMapped() setter to match the
IsMapped() getter. Before you had to reverse your logic on a few of the
flags (in this case, using SetIsUnmapped()). Not impossible to use, but
not immediately obvious and intuitive, and hard to remember when to use
the opposite setter. These older methods will remain available, but
should be considered deprecated.
commit 9cee14686c62b841e9a3ed08793aac18d9d40369
Author: derek <derekwbarnett at gmail.com>
Date: Tue Dec 7 13:02:24 2010 -0500
Fixed: handling BamAlignments with limited char data
commit d9088d1c37ada9d748ac5ee8cefc2e773621566e
Author: derek <derekwbarnett at gmail.com>
Date: Mon Dec 6 16:30:13 2010 -0500
Fixed : improper exit code from FilterTool
commit 8749b649779b660c20226581328c078b99c4d37f
Author: derek <derekwbarnett at gmail.com>
Date: Mon Dec 6 12:02:18 2010 -0500
Fixed: core mode setting for BamMultiReader::Open() in FilterTool
* Was opening with coreMode=true, which caused errors filtering the
first alignment's char data
commit 7664c745b7787707501ca7ee5bf412ceff2d39b8
Author: derek <derekwbarnett at gmail.com>
Date: Sun Dec 5 23:11:03 2010 -0500
Added new RevertTool to the toolkit
* "$ bamtools revert ... " will clear the IsDuplicate flag on
BamAlignments and replace the Qualities with the contents of the OQ tag.
* Suggested by and draft implementation contributed by Al Ward.
commit 4782d394d544d459fe7badd5f803490f0a48f8c3
Author: derek <derekwbarnett at gmail.com>
Date: Fri Dec 3 15:45:20 2010 -0500
Fixed: bug in the BamReader::Jump() codepath, specifically the
BRP::AdjustRegion() logic
commit 369e2de20a6d939d07ffc09462167a3b688bbdde
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 22 13:02:38 2010 -0500
Moved private implementation API files to internal directory for clearer separation. These should not be included by client code
commit bc876d9d1f57c3c14fba29827a74e858ee527ee4
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 22 12:48:00 2010 -0500
Added proper import of bamtools version info from CMake
commit b5e14489be6687825572d6c252f477472021e78c
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 22 12:47:10 2010 -0500
Fixed BamRegion bug: previously only checked if refID was -1, needed to make sure all negative values were invalid
commit 6f3fff23561d95067651931a8768c6466cabe99f
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 15:52:04 2010 -0500
Continued breaking up of monolithic classes: extracted BamStandardIndex & BamToolsIndex into their own source files.
commit 5620c041157d4b1cdbf8f5d5d1ce8fdf590cbfbe
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 12:41:54 2010 -0500
Extracted BamReaderPrivate & BamWriterPrivate from inner classes.
First step in breaking up the API's monolithic classes. Should allow easier maintenance, testing, and adding features as we go forward.
commit ced2983817b0efe2c4ea08ff1479937ea9131017
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 11:14:54 2010 -0500
Added UTILS_EXPORT macro to classes in BamTools utility library
commit e24bc523b0bd086dbfad7165901b2237b5d64316
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 11:01:58 2010 -0500
Added API_EXPORT macro to classes in BamTools API
commit a491919dfa406b3b6b3fa58d51cbd36eb7473da6
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 10:42:40 2010 -0500
Removed commented (library export) definitions from utils & jsoncpp CMakeLists files
commit 4c9d2fdc9c556713531bdd2f25ce49685ab218e9
Author: derek <derekwbarnett at gmail.com>
Date: Fri Nov 19 10:32:45 2010 -0500
Migrated to CMake build system.
* Please see README: Installation for help in building BamTools toolkit & API and integrating the new shared library into your application
commit c5363861478f495b41a2ad99028326f85feeb905
Author: derek <derekwbarnett at gmail.com>
Date: Wed Nov 17 19:41:29 2010 -0500
Changed GetNextAlignmentCore() calls to GetNextAlignment() in FilterTool
commit 0abdf800c25b306eb2f494d4f3516b598ae82b2d
Author: derek <derekwbarnett at gmail.com>
Date: Mon Nov 15 14:54:27 2010 -0500
Minor formatting cleanup
commit 3955b599537c7168a567644f48701e15185ef662
Author: derek <derekwbarnett at gmail.com>
Date: Wed Oct 27 12:54:38 2010 -0400
Removed more non-standard STL calls from BamIndex.cpp
commit feb0790a223926ac4d19da87c2c8ba6b015640af
Merge: 49b3a8d aa629bc
Author: derek <derekwbarnett at gmail.com>
Date: Wed Oct 27 12:33:56 2010 -0400
Merge branch 'master' of git://github.com/ekg/bamtools
commit 49b3a8dde8b9cfc107a8a59370bb2557ee202060
Author: derek <derekwbarnett at gmail.com>
Date: Wed Oct 27 12:32:16 2010 -0400
Removed non-standard stl::map method calls
commit aa629bccb3853eca6ae74a6de76ef5c02bc97f9a
Merge: 636c2ab abb3c1a
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Oct 27 12:08:22 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit 636c2ab1acd0005f652829cdd5d5c0b67074c88a
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Oct 27 12:07:47 2010 -0400
clarified no-index behavior in bam multi reader
commit abb3c1abf0301481545a24445ad2bd4263fceb2b
Author: derek <derekwbarnett at gmail.com>
Date: Mon Oct 25 14:10:42 2010 -0400
Updated BamTools version information.
* Also automated version information propagation forfuture updates.
Only need to set version in top-level Makefile.
commit fe07d12a66f7a43128e3417c95a44732b831e97a
Author: derek <derekwbarnett at gmail.com>
Date: Sun Oct 24 15:26:15 2010 -0400
Updated README
commit 89028c85b3db7b4eb55c40fabfcb9c55a0d168d9
Merge: 5b767c6 2b0d33f
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 17:15:07 2010 -0400
Merge branch 'master' of git://github.com/ekg/bamtools
commit 5b767c69c0660eb9717ce7965f8e2009bd275732
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 17:14:44 2010 -0400
Updating README... still a work in progress
commit 2b0d33f6c1aa259c117584313da93e2f76231f68
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Thu Oct 21 17:03:48 2010 -0400
add index caching mode setter to BamMultiReader
commit 404ea83ee6e81411bea0ea39f852bb7e68767a8e
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 15:00:03 2010 -0400
Fixed NoIndexCaching behavior
* Previous commit lacked the post-jump dump of index data when this
mode is selected.
commit c96c024ebf583c792a3728e54766a00a5eb9a803
Merge: 3a975af fa8d485
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 00:22:36 2010 -0400
Merge branch 'master' of git://github.com/pezmaster31/bamtools
commit 3a975af617ffe4f1f8077e7e45fa484296f5e704
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 00:19:40 2010 -0400
Implemented index cache mode for both BAI & BTI formats
* Client code can now decide between 3 index cache modes:
Full : save entire index data in memory
Limited (default) : save only index data for current reference
None : save no index data - only load data necessary for a single-
* Required a major overhaul to BamIndex interface and derived classes.
Lots of refactoring to move common code up to BamIndex.
Derived classes now share much of the same method names &
organization. Only implementation details differ, as needed.
* Miscellaneous: moved BAMTOOLS_LFS definitions into BamAux.h & cleaned
up BGZF.h
commit fa8d485d67c1a88d44e596ae430b41797a70cb1a
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Oct 21 00:19:40 2010 -0400
Implemented index cache mode for both BAI & BTI formats
* Client code can now decide between 3 index cache modes:
Full : save entire index data in memory
Limited (default) : save only index data for current reference
None : save no index data - only load data necessary for a single-
* Required a major overhaul to BamIndex interface and derived classes.
Lots of refactoring to move common code up to BamIndex.
Derived classes now share much of the same method names &
organization. Only implementation details differ, as needed.
* Miscellaneous: moved BAMTOOLS_LFS definitions into BamAux.h & cleaned
up BGZF.h
commit 0c50d5abdc43df228147df3e3fb166b78b303fe9
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Oct 16 16:45:08 2010 -0400
modified/clarified some help & usage messages
* (also a test run for different git commit system on my end)
commit d553a62a6dda3377021f51ad172b7a5bc5fab412
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Oct 9 19:54:03 2010 -0400
Changed BamAlignment::SupportData from private to public.
This should remove the access-control errors that occur when building BamTools with older, less-conforming compilers
commit a276e3f3926309a9b566bed52ccb8aba9ee334f3
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Oct 9 19:28:42 2010 -0400
Fixed: bug(s) related to empty references and regions.
* NOTE - This fix does introduce a slight modification to the *.bti index format.
So any existing BTI index files will need to be rebuilt to support the bug fix (apologies).
commit 8fbe195817a362ae99f0630bcf9e4e9bb6db990f
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Oct 5 11:15:50 2010 -0400
Minor formatting, commenting cleanup
commit f94cc4961247ab5ee55aa99987e70ef86107db40
Author: derek <derek at donatello.(none)>
Date: Mon Oct 4 13:49:10 2010 -0400
Added tag support in filter tool.
commit 8807d4776b73d173b10cf6fb77ccbf485d270597
Merge: c2c1d8a 4213425
Author: derek <derek at donatello.(none)>
Date: Mon Oct 4 10:25:30 2010 -0400
Reviewed BAM to YAML conversion contribution (thank you Chase Miller). Reorganized to fit BT code style & structure.
commit c2c1d8a5d8444b30b8af2a4bbb291ddab059be2d
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Sep 29 16:23:56 2010 -0400
convert: cleanup of prior fix, report if no index file found
commit 229a33c5e9e6b17a7d8c19d3c37382d6e5fc0605
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Sep 29 11:54:48 2010 -0400
prior commit caused bug with convert
Fix: attempt to open indexes when we are not reading from stdin.
commit 7398af8e2fd283fccb47945116a001010e940c91
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Tue Sep 28 17:44:29 2010 -0400
exposes cigar string data to bamtools filter
commit 2b99e4788a395d5cde8c7d857fa5c6532b6222dd
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Tue Sep 28 17:44:12 2010 -0400
added reader.Open checks to a number of tools
commit 421342508d90ee06aa9973a191f52667971072c6
Author: Chase Miller <millerwz at snp.bc.edu>
Date: Tue Sep 28 11:16:13 2010 -0400
Added Yaml for outputing BamAlignments.
commit c7985cc75125f752361cc1915ac32e5b9d40a0d3
Merge: e929b8b a97aada
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Mon Sep 27 22:23:27 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit a97aada254953e7ef30287f173c25a25e02c3815
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 23 15:56:43 2010 -0400
Fixed lack of reverse complemented output in BAM -> FASTA/Q conversion.
* Also appended '/1' or '/2' to paired-end FASTQ entries to indicate which mate it represents.
commit e929b8b81a31b0bd02530ae273fc795db70314ea
Merge: b754928 c66ba83
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Thu Sep 23 10:30:09 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit c66ba836246a1eada3557a5c8dcc9d3558ed093b
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Sep 21 22:00:14 2010 -0400
Implemented 'compound rule' logic in the FilterTool's script support.
* Previously the script was limited to doing 'OR' comparisons on various
property sets (what I call here filters). Now, by providing each filter
with an id, you can use these id's to define a compound rule.
* Documentation is severely lacking on this end at the moment, but I hope
to have a good explanation up soon. I think this interface could provide
a powerful flexibility in querying BAM files for very specific cases for
further analyses.
commit 4a72c95050cfa5bf0c891b13fd9504ad301ca559
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Sep 20 11:35:16 2010 -0400
Cleaned up SplitTool internal implementation. Use of template methods should make maintenance a bit easier.
commit b7549281cadae48219dd42fb93a14524b35fdb0f
Merge: 824ecac c98f4ce
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Mon Sep 20 08:33:39 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit c98f4ce3c7c19af972f58eaf0053b94ba9413c81
Author: Derek <derekwbarnett at gmail.com>
Date: Sun Sep 19 17:06:02 2010 -0400
Removed a backup text file that snuck into an earlier commit
commit 11b57b2ad4d39c9140d35674600dc4a4ff658261
Author: Derek <derekwbarnett at gmail.com>
Date: Sun Sep 19 17:05:16 2010 -0400
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.
commit 5ad5339ceee660c5998c1fd47cb709448e94ee75
Author: Derek <derekwbarnett at gmail.com>
Date: Sun Sep 19 17:02:17 2010 -0400
Added GetTagType() to BamAlignment
commit f7adbb985b07a32e2ab53c783a040dd290deada0
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Sep 18 16:47:34 2010 -0400
Updated to match new BamAlignment.h includes
commit c7619610b682e733bca5b3204c49405f5fbee911
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Sep 18 16:45:29 2010 -0400
Missed api/Makefile in last commit.
commit 049d6b2501ea9c9afeb8588013d5f536246a2ca8
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Sep 18 16:43:37 2010 -0400
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.
commit 824ecac29bfd739f996aea108a5597d9a564df57
Merge: 9e7f316 89dbe0f
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Sat Sep 18 16:04:58 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit 89dbe0f38482e43f5e49d9cc5c8670ec00f3f53f
Author: Derek <derekwbarnett at gmail.com>
Date: Sat Sep 18 00:42:23 2010 -0400
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.
commit 9e7f3168db0c2473674f33a66eb63dedba0353f8
Merge: 0ef88b9 7124011
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri Sep 17 11:30:59 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
Conflicts:
src/api/BamIndex.cpp
commit 7124011e66fb0345c57b6f6046527049fda9f461
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 16 01:52:26 2010 -0400
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
commit e9617e555c77b5b58da1959e18e6421fa5f271a9
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 16 01:47:58 2010 -0400
Did some housekeeping in BamAux.h - moved some constants to the files where they are actually used.
commit 1ec34c31512b530948037ebf34e072a50f0db5fa
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 16 01:41:03 2010 -0400
Missed an update to BamToolsIndex code in a previous commit
commit 5f5d20647f918069e0b6dbc055ea184c37bd1196
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 16 01:37:28 2010 -0400
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
commit 02a90ba6b35ce74cbb5e9b49403c6f1cb046afae
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Sep 15 11:48:33 2010 -0400
Added option for users to specifiy half-open (1-based) return value for BamAlignment::GetEndPosition(). By default, returns 0-based coordinate after recent modification.
commit 0ef88b963e167f9d66fe9e55d9c22c3863498b29
Merge: ccd532b 7eee951
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Mon Sep 13 15:10:08 2010 -0400
Merge branch 'master' of http://github.com/pezmaster31/bamtools
commit 7eee95124eb52bee48d75bbbfc5ab5f2720bfe63
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Sep 13 14:50:05 2010 -0400
Fixed off-by-one error in BamAlignment::GetEndPosition()
commit ccd532ba03f9ef6a5fa8cb18c2da58f79e0b4ae0
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Sat Sep 11 13:27:30 2010 -0400
updated debugging output in BamIndex, seek vs. calculate distinction
commit c1f2fcd24b981996e933267541de9a2972277db3
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Sat Sep 11 10:55:22 2010 -0400
Added more verbose debugging output to BamMultiReader::SetRegion
commit 4bff07c63b54d5eeecfe9c0fa63489e3ac73883b
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Sep 10 17:38:03 2010 -0400
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.
commit 389b0cc9b4d339c6a2f3f56622cf90f7039e58d4
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 9 23:45:21 2010 -0400
Removed debug output statement that slipped into last commit.
commit 62b1c71c1d824b6d37b029ce67133f42f2563d78
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 9 23:42:04 2010 -0400
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.
commit 0043e2dd10151e457731e477b2efc8c3c24e27c8
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Sep 8 16:17:20 2010 -0400
prefer bamtools index in BamMultiReader
commit 90bb3691f9aa2a2e8a4dd906c2439c7bc434eb78
Merge: 1ee9b6b 1d03f81
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Sep 8 15:36:39 2010 -0400
Merge branch 'master' of git://github.com/pezmaster31/bamtools
Conflicts:
src/api/BamReader.cpp
commit 1d03f81d725ffedeac9d9d73a2058f00cfc0b0e4
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Sep 7 14:42:03 2010 -0400
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.
commit 1b19b64a28c1a892f2fcbb00b111853c5e8a2f8e
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Sep 7 14:30:08 2010 -0400
Documentation update
commit ce6b127bd2921f1dc137eb296190d0f4fb686d17
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Sep 7 13:24:56 2010 -0400
Added -region option to bamtools_merge
commit a9a9b2d45cf3417c28be9ac30ef51b16ce1875f6
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Sep 7 00:56:03 2010 -0400
Previously missed a line in BamReader.cpp with the recent index overhaul.
commit f0bc238bde22f2fdda922dfee8fca9e37995f2e9
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Sep 3 17:14:05 2010 -0400
Large-scale API indexing re-organization:
* Moved FileExists() to BamAux.h so that all API classes have access to its functionality.
* Created 2 'factory methods' in BamIndex.h to return a BamIndex subclass, depending on client\'s specified PreferredIndexType & on what files actually exist on disk.
* Renamed BamDefaultIndex as BamStandardIndex. Hopefully this name should be a clearer description going forward than BamDefaultIndex, since the standardized index may not always be the 'default' in every situation.
commit c3de50d70f8296f2b24316472bda4a053dd69e37
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Sep 3 00:40:11 2010 -0400
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.
commit 164366c9fd23717e4b7279518eecaa32baed502c
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Sep 3 00:37:39 2010 -0400
Cleaned up index file handling throughout toolkit. Did this by adding a FileExists() methods to BamMultiReader for determining which index file to load.
commit 3b6edd753c52123d553151400443035f915637b9
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Sep 3 00:35:05 2010 -0400
Added IsIndexLoaded() public method to BamReader. Allows client to make sure index data is available before attempting any random access ops
commit 43e7b12a27aec2e6ebcbd87959e1161013c5d0ed
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Sep 2 15:58:06 2010 -0400
Modified help description for -bti option
commit b1c4035f6ff27e9a04673bfec77b234d99aa5def
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Aug 31 23:09:20 2010 -0400
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
commit 32ad5a7c3cf34ddc0f4d38b12fc5112386122e45
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 18:53:59 2010 -0400
Posted implementation of FilterTool.
commit c33546e0647048a290814d64937a709f33264468
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:17:32 2010 -0400
Minor formatting & commenting update
commit 848e2fad110ddebc6de34f65b89954039fe50a85
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:12:23 2010 -0400
Updated bamtools_utilities with #defines
commit fa5e8b2f5a1f6e57e8b037484d86e009bf699352
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:11:14 2010 -0400
Updating bamtools_options
commit 615a9c9407bb40db133c3d8c09339dc01cae578a
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:08:09 2010 -0400
Added bamtools_filter_engine.*
commit b94b461ee40d35b4db475da6bde6af6db046658e
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:05:50 2010 -0400
Removed -pg debug flag from Makefile CXXFLAGS, accidentally incorporated into a prior commit
commit 1764cc8f218686570108feeecd207971e33a7dfa
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 16:04:04 2010 -0400
Forgot to add jsoncpp/json.h in a previous commit
commit 3e379f039c8eaffd32df66732be04bee1f8c9ed3
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 15:57:55 2010 -0400
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.
commit 471cc423d37f1a3ed02cac0108ba04e5e984344f
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Aug 30 15:55:20 2010 -0400
Added JsonCPP code to repo. Will be used by FilterTool for script parsing
commit 1ee9b6b3d98a4bfd5a60c583bc7847c545a60e32
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri Aug 20 12:22:34 2010 -0400
change printf's to fprint(stderr,
This pushes errors to the expected output, stderr, instead of mixing
them into the standard output stream.
commit 03a51f0e4051764b08a4226358b77159c5a2152e
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Aug 18 15:59:10 2010 -0400
Missed a Makefile in last commit - just adding header comments
commit 4461c9d81ec5a1c61a2c121f261b5eb504381b21
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Aug 18 15:56:58 2010 -0400
Added simple header comments to all Makefiles, to help distinguish between them easier
commit f8d828f713203226f9cd58db046c7b767d4b78ad
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Aug 18 15:28:51 2010 -0400
Modified Makefile to ensure creation of bin/ and obj/ directories
commit 0180d7256f5c781364b04559b39ed2db41585787
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Aug 18 15:19:08 2010 -0400
Reorganized source tree & build system
commit acdea352102b176dc519f6cbdd7980d1041079c2
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Aug 17 21:51:51 2010 -0400
Minor formatting cleanup in BamIndex.*
commit 2d6d143e041a08c2083a6857898ca36753317dad
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Aug 17 16:39:44 2010 -0400
Modified the way BGZF sets up uncompressed output. Modified BamWriter to support uncompressed option.
commit 6222ce815dc4cb69d5d4c276cb435087e1cd77a8
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Aug 17 15:19:10 2010 -0400
Modified BamWriter::Open() to return bool on success/fail - was silent before, so clients had no way of handling errors
commit 2dded2f908d2666f47940c0788bb825cf4da6130
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Aug 17 12:04:51 2010 -0400
Added write-uncompressed flag to BGZF. Commit includes some other formatting cleanup as well.
commit 8c7de7c0ea6667056be7b81f83480c5ce925981e
Merge: cc07ff1 62c1034
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Aug 6 11:35:50 2010 -0400
Merge git://github.com/ekg/bamtools
commit cc07ff1c008d2182793478971d71d7e0ac45c058
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Aug 6 11:35:43 2010 -0400
Minor formatting cleanup: really just an update to be able to pull in Erik's JSON changes.
commit 62c1034f56e918f277bf9ee1ad5afde5a654bf88
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Thu Aug 5 09:01:02 2010 -0400
for json output in bamtools convert
Process qualities to provide a list of Q scores in the json output
instead of just a string of characters.
commit c50fd68f6f1eec78d0c8b2558093ad6305f862b3
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Aug 4 16:03:07 2010 -0400
Bug fix in BamReader::Jump()
commit 9d0a3d3a733ff4c4a662ddef52ee476144d50440
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 27 12:52:58 2010 -0400
Added AddTag/EditTag/RemoveTag methods to BamAlignment. Refactored existing GetTag methods.
commit 3d3f61f4545aab4a5bc8ca9170bd4dc9ff68ad81
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 23:10:54 2010 -0400
Reworded bamtools stats general help description
commit 113d4fe3564c2001d0a11b7f7e7bccbfd70cbb79
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 23:09:58 2010 -0400
Mostly cosmetic fixes. A few tweaks to subtool options/settings naming or default handling as well.
commit 511ee6cca3a0a8b8aca697bf575e8c41d07f8ab8
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 22:58:15 2010 -0400
Implemented basic alignment stats (count/%) for most of the alignment flags
commit 344deb0be8f4cc5db83cdfe7b31b9e8276ff677c
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 14:24:54 2010 -0400
Various cleanups. Added -noheader to SAM conversion in ConvertTool
commit 35cccd93c535d7b82bb6e0a08b9992adff9cbd9d
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 14:23:48 2010 -0400
Forgot to update Makefile with last commit
commit e395da75904f3b0afc2629219770f889e31ee679
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 14:23:14 2010 -0400
Removed SamTool (bamtools sam ...) from toolkit. This functionality is covered by ConvertTool.
commit f302be8995b9b775f9203711c27e8cc6750f830e
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 12:18:16 2010 -0400
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.
commit 9a23e1862003047b0c236ae1ea739a111bdbc797
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 22 12:16:06 2010 -0400
Fixed: remove unnecessary EOF write attempt for read-only files in BGZF::Close()
commit e3a49e63c07cc4776c769eec9ca6a2d99718154f
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jul 21 11:00:44 2010 -0400
Forgot to include updated bamtools 'main' with RandomTool commmit.
commit feaa1d36ff333c224153ba90330daadd5d104cef
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jul 21 10:48:04 2010 -0400
Added the <cctype> include to BamAux to explicitly support the toupper() fxn. It had slipped past newer compilers so far
commit 2825eb5ba611c7e5b562ad5eafb78deee6b03420
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 20 18:34:31 2010 -0400
Fixed fopen-related typo in bamtools_fasta.*
commit 6f3ae10b7a7c002f32d3bf789153e546d11462fd
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 20 16:28:31 2010 -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
commit be0639f742c5df63e830a6a4176ff964a04c0f06
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 20 16:25:48 2010 -0400
Modified BamMultiReader::Open() to return bool. Still needs some tweaks to handle all error cases correctly.
commit aea2ee257728846a31535ba367da7e7d14a2fa7c
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jul 19 19:05:51 2010 -0400
Added cross-platform LFS for tell/seek. Removed fopen64/freopen64 - hopefully unecessary with -D_FILE_OFFSET_BITS=64 compiler flag
commit f6288f9f90747418a5d3c61b7713bee8e3a16112
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 15 14:04:16 2010 -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.
commit 8e67ee2fda266e4c315bbd5688c341f827357251
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 15 13:59:42 2010 -0400
Modified Rewind() to check actual data present when resetting region markers, instead of relying on potentially incorrect RefData::RefHasAlignments
commit a2400c1ecfd075271b14c2c83aae0dc42bf7e42a
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jul 15 13:44:53 2010 -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.
commit f68dccd9031c84f73b9754c1fbced63bd8551f6f
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 13 12:00:42 2010 -0400
Purely cosmetic udpate. Cleaned up some commented blocks, added file header information (author, description, etc)
commit b4291142870c32a1c5db4d1f0a8b4640d4a5d5e2
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jul 13 10:47:17 2010 -0400
Updated Makefile for fasta & pileup
commit ce1a192b46d5d84c7d6c9c81c868dbaf46d79edd
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jul 12 21:57:40 2010 -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
commit 4aea04656e2666bd568cd9bf59b22b635cf1aef5
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jul 12 21:53:57 2010 -0400
Begun basic pileup conversion
commit 883bc9dd6d4fb24965c51d6d1b9b73d6c229f390
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 15:29:17 2010 -0400
Added simple PrintBed() method; plan to add PrintWiggle() next. Added use of function pointer to clean up code for conversion method selection.
commit 9c22d5ad7a9900667e5a1a6f88730ed92c20f472
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 13:02:07 2010 -0400
Fixed typos in last commit.
commit f7ce1f11dc76fe0d74e0bf44e98c06017ae25898
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:57:55 2010 -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
commit a00339bed19ef587e28e9391cf21a63266fea66e
Merge: 0c7d3b7 155ba46
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:28:22 2010 -0400
Merge http://github.com/ekg/bamtools
commit 0c7d3b7c86c2eb2b71b4fa5949828cedfb890d00
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:20:39 2010 -0400
Fixed: proper handling of BamAlignment::AlignedBases when QueryBases is empty. Thanks to Aaron Quinlan for catching this.
commit 9f32927e1a745cf27af58867f7182f6ee2e26ed8
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:08:31 2010 -0400
Updated index and count sub-tools to recognize new (.bti) index file format
commit 9c0245facde1cd542ca59d66082b3525ad897af3
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:06:27 2010 -0400
Separated indexing ops to new class. Implemented a fixed-partition-size index format (.bti) as an alternative to the BAM default (.bai)
commit 78a223dbe7949c65cfc16d972ef84f4a62351fc7
Author: Derek <derekwbarnett at gmail.com>
Date: Fri Jul 9 12:04:07 2010 -0400
Enforced proper handling of large files (>4Gb) on 32-bit systems.
commit 155ba46a7dc23b749cc353b194f7ae6336f9f23d
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jul 7 15:54:39 2010 -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.
commit 2ffdeb8efe1f8e7b3f3152034ee6ea643200dbb3
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jul 7 15:32:48 2010 -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.
commit 4f2d10233ddb00dc6f1bc39150bd3b8aa3052418
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 28 15:14:12 2010 -0400
Removed accidental commit of .o files
commit 5580b247bf3ef7b0cd1afd3aa16dc15cd7523636
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 28 15:10:28 2010 -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.
commit 2498eeef5404327a4914de39bec6ab8a6d149462
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 21 23:17:38 2010 -0400
Updated temp file path stubs to reflect input BAM file stub, so that simultaneous sort runs don't interfere with each other.
commit a9e3b2afa1a84d7d92bb54e5c99b6ff341c1328a
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 21 22:23:32 2010 -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.
commit 0108fd0bf864c11355a3c7e39d33dcf6d7a149d2
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Mon Jun 21 11:56:39 2010 -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.
commit 12c10ab962401b7da243d59cba821a8bb06d65ec
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri Jun 18 15:13:46 2010 -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
commit d9d6a31a36b6738199c4cc3992be8f3cc6db36df
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri Jun 18 11:31:34 2010 -0400
moved bamtools_count to use BamRegion
This is more consistent than using a bespoke struct (Region) with the
same fields.
commit 7f701a076169ceecca08b5d5d9bc8b5deebc8350
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 17 17:35:27 2010 -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.
commit 37d0847676180478a7ffee0f2c121c6e02f1c95b
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 17 12:31:29 2010 -0400
Modified BamReaderPrivate::GetOffset() & BinsFromRegion() to make use of right bound cutoffs
commit 875e038830304b62dfcc80719208b7494ec83681
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 17 00:01:56 2010 -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.
commit 54b237d50703e5c5c2a541fe425637446354f769
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Thu Jun 10 13:33:28 2010 -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).
commit 5e3a115ed6c8bd643d59f0a8fa82201d6d733a47
Merge: b6a5bf3 41da743
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Thu Jun 10 09:23:36 2010 -0400
Merge branch 'master' of git://github.com/pezmaster31/bamtools
commit 41da74387a2c1db662a416d20d7150ec1a745212
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 10 00:50:37 2010 -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.
commit b6a5bf305b6548020db260ed89e263a946b90897
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jun 9 12:06:13 2010 -0400
further cleanup of duplicate @RG tag warning reporting
commit 234da1cfa68fa6ea6616ffeb293f3a53c4d5388b
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jun 9 11:46:46 2010 -0400
added warning for duplicate @RG tag in header
commit c1a31e056e6867ada6f18baaff983f932e8f1177
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jun 9 09:39:07 2010 -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.
commit 875f0cdc2eeaa1c1d35d1e8bee1e27f8150f1092
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jun 9 09:31:01 2010 -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.
commit 5ca1303304066dbb42207d79c6d1703377908e0b
Merge: aa89df8 e4f1246
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Wed Jun 9 08:39:07 2010 -0400
Merge branch 'master' of git://github.com/pezmaster31/bamtools
commit e4f12462a1553230cfc9ef1474d46803fb9e9c92
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jun 8 23:42:03 2010 -0400
Removed accidental add of object files
commit c8518cde9e4def44b657b34eee23096bb7bdcb00
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jun 8 23:29:45 2010 -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.
commit aa89df8c4510f88b2101ce91e8c46b99387560bd
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Tue Jun 8 16:28:58 2010 -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.
commit 12d1865e534b6561d0becb68afef351ebf0f74f8
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Tue Jun 8 13:05:59 2010 -0400
json output
commit 0c1c99f07953970d1a160c4be407522f7775bd7f
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jun 8 12:32:02 2010 -0400
Fixed output of tag types c & C. Removed atoi() call. Simply casting the single byte to int works correctly.
commit 73433cf4992127c558e72cf75147a9e599330d3f
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 7 16:18:10 2010 -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
commit 0f2cbac53545e212a02f190d515c33d9b066cacd
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Mon Jun 7 15:25:25 2010 -0400
pass ostream variable to print functions in convert
commit 82ded957c29023424742e76084b8aa6f2ee0cb2c
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 7 13:58:46 2010 -0400
Began rolling over bamtools_sam into bamtools_convert. Kinda hacky setup for now, but ok to get conversion routines tested
commit dac30b06e53e46cfd4efb0d2d4f771b0202e09d9
Author: Derek <derekwbarnett at gmail.com>
Date: Mon Jun 7 13:24:51 2010 -0400
Fixed typo in settings config.
commit ab184573bd40b8358cc3f6b306423c187f1a24a4
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 16:02:51 2010 -0400
Added ConvertTool.h/cpp. Not yet implemented.
commit f1dcf39dd1243321385af7c9bc152174cb787c6e
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 15:28:43 2010 -0400
Updated README
commit eb97bf5f91acd9a1ce2964e60a79fecffd9f6d72
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 15:27:02 2010 -0400
Added FilterTool.h/cpp. Not yet implemented.
commit 80215a39a701ab6241b7761a3ea92477a503af7e
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 13:42:31 2010 -0400
Added a second Utilities::ParseRegionString() that accepts BamMultiReader
commit 44ac262d02ef007262d7504e963234329245dc5f
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 13:34:13 2010 -0400
Cleaned up CountTool, by extending Utilities::ParseRegionString() to also do validation. Should be useful for other tools using REGION strings
commit 20e692c4a06c181ff7216c00d5808966210e47c9
Author: Derek <derekwbarnett at gmail.com>
Date: Thu Jun 3 12:30:15 2010 -0400
Minor formatting/commenting fixes. No major changes to actual code paths
commit aba2821a7ffdc8d9f86e63fd1895c8e642c93ed4
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jun 2 23:52:07 2010 -0400
Implemented bamtools sam. Required new unpack methods in BGZF.h. Seems to pass all files tested, compared against samtools view output
commit 25b5870b880bd307a86067ec92c88c2cdf127f67
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jun 2 14:22:57 2010 -0400
Removed a debug output statement that piggybacked into the last commit
commit 0a62b75d4a37e7f6bb0b45ff3eff3c0d1369e067
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jun 2 14:13:24 2010 -0400
Implemented CountTool, cleaned up MergeTool.
commit 32890f0650b5ec57a9cff10f1a9512047e7a168a
Author: Derek <derekwbarnett at gmail.com>
Date: Wed Jun 2 12:06:43 2010 -0400
Put utilities into own class with static methods
commit ca4a8df663c33d8b62536558022931b31408c411
Author: Derek <derekwbarnett at gmail.com>
Date: Tue Jun 1 22:54:30 2010 -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
commit 81bbce8a213e07867470b8b01d5b2fae0e1cb668
Author: Derek <derekwbarnett at gmail.com>
Date: Wed May 26 22:25:39 2010 -0400
Mostly cleaned up help & usage messages. Added MIT license.
commit aa45b408b8ce3f760f4bb5b79a9fad648c245437
Author: Derek <derekwbarnett at gmail.com>
Date: Wed May 26 16:17:14 2010 -0400
Removed BamTrimMain.cpp. Missed that one in last commit, removing the old 'toy' examples
commit cebdcc01b264653dc17227b6b2391645661e978a
Author: Derek <derekwbarnett at gmail.com>
Date: Wed May 26 16:16:03 2010 -0400
Removed BamConversionMain.cpp and BamDumpMain.cpp. No longer needed if toolkit available.
commit cc115ec7bf51575284b1ad17cb69e32602267158
Author: Derek <derekwbarnett at gmail.com>
Date: Wed May 26 16:09:15 2010 -0400
Removed bamtools_test from Makefile. Was a temporary, local test harness only
commit d37b45d132eb330a2c918c59e9ecb78168a4ac47
Author: Derek <derekwbarnett at gmail.com>
Date: Wed May 26 16:05:15 2010 -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.
commit 8a0328ccbd7db4283b113e1f3480fd5ac334dbbc
Author: Derek <derekwbarnett at gmail.com>
Date: Tue May 25 13:12:27 2010 -0400
Added templated GetTag() method, compile tested, but not runtime tested
commit 320649eff43c8092ce9ef548179905dccfeb1c42
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri May 21 17:07:31 2010 -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.
commit 77f7ccd20d2a255f5f2f4200b458500144551ad6
Author: Erik Garrison <erik.garrison at bc.edu>
Date: Fri May 21 16:53:26 2010 -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.
commit c1c9ffba877a2df572fe7e0cc1eaa2019d7157e0
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri May 7 21:15:38 2010 +0000
Removed Boost dependency in BamMultiReader.cpp
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@52 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit da8310a92e91d3682857b8f9affbe19621ea7bae
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri May 7 03:10:38 2010 +0000
Didnt actually add BamMultiMerge and BamMultiReader with last commit. Adding to repository this time, seriously.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@51 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 68af22063ff54963fd195cab7daf58c4605629e0
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu May 6 19:30:12 2010 +0000
Added BamMultiReader and BamMultiMerge
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@50 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 1537d0266677d03a65d5b15b9a6e4d4a063c5163
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Apr 14 16:32:52 2010 +0000
Moved BamReaderPrivate::CalculateAlignmentEnd() to BamAlignment::GetEndPosition() to expose it to the public API. Reorganized BamAux.h to look cleaner and facilitate quick lookup of available data and methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@49 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit c40c7fe13bf51c3aa5bd1dcfa7bcf4c580e4137c
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Apr 6 19:30:32 2010 +0000
Major speedup of BamReader - removed full character data building until alignment actually requested
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@48 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 08a9a3bbbc8cf0d39eb2a284eaf955743f6deb11
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Mar 31 18:41:40 2010 +0000
Updated BamAux modified date
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@47 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 3d193b496bf6a5f1b276dd5c78369d7413dc7a17
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Mar 31 18:37:25 2010 +0000
Restored BamDumpMain to old version without dumping tag data
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@46 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit fd6ca20fb63a49b46a0e97e5c47402bc307b57f1
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Mar 31 18:36:11 2010 +0000
Major fix in handling tag data in BamAux.h... checking for null characters in BamAlignment::GetReadGroup() and similar methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@45 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 75fc609c00581bf98d2340b88766b2356751571c
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Mar 31 17:54:16 2010 +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 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 78c56aa6066d41c7c63541eafb60c9162c291c0f
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Mar 31 17:40:13 2010 +0000
Modified BamDump to spit out TagData (for debugging)
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@43 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit b3477d029914521bb7058941ea837a00144bd512
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Mar 30 15:39:47 2010 +0000
Updated contact info in README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@42 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 5ccdabf3912d6468bbd907442a6ab5b1da858c34
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Mar 30 15:36:55 2010 +0000
Had some typos in last commit. Fixed.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@41 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 74536d1d4177b7527b8a0d1c1e95b22e233b8300
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Mar 30 15:00:57 2010 +0000
Fixed: off by 1 in BamWriter, variable tag parsing in BamAux, endian-correctness
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@40 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 9a8d3e6e4305daff54da7e1626b7ab67629aae11
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Mon Jan 11 19:10:15 2010 +0000
Added #include<cstdio> to BamAux.h to cover use of printf. Added AlignmentFlag setter methods, per request by Aaron.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@39 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 18ffb7f0815a9311739d620b5f9227c2460ab0be
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Mon Jan 11 15:11:15 2010 +0000
Fixed fread() related compiler warnings. Fixed std types [u]intX_t errors (used, but not defined in BamAux.h). Added Aaron's stdin/stdout read/write feature.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@38 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 77016748525395a5953dcf71688d68ff06130228
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Jan 8 19:55:45 2010 +0000
Updated BamAux
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@37 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit b5a48a0f4227c39c4cea4e67a427059a3e952cd6
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Jan 8 18:42:30 2010 +0000
Added empty block EOF to BGZF::Close
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@36 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit d602e73b629c7180ddcd27bb8e3c47aacbb74e04
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 19:10:52 2009 +0000
Fixed README typos
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@35 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 79551a3b399f0d3935a9eaf317859a30a11922cd
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 19:10:18 2009 +0000
Updated README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@34 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit b0b7a648d074a5852e1012d48927efe04c7be934
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 19:02:04 2009 +0000
Fixed a few more signed/unsigned issues
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@33 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 0d00f380644c78a321e8891562bf165317af10b4
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 18:57:41 2009 +0000
Fixed some signed/unsigned int issues
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@32 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 8a80c879c3e8fb77e484952540c304a7fd3c0879
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 18:42:22 2009 +0000
Updated Makefile
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@31 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit a434db60a2ba1c77a0084704290c0e2ba6dcf1dc
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Dec 8 18:37:03 2009 +0000
Major overhaul to BamTools
Separated out Bgzf routines to BGZF.h
Simplified main BamReader.h/BamWriter.h headers, by adding pimpl
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@30 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 1e8d9a6732361a056b13aaa4f5a8e9f824f84899
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Oct 1 04:13:22 2009 +0000
Fix of signed/unsigned in BamReader methods
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@29 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 6f110ab8488bc8c6073561028dd5f386f9b4172a
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Oct 1 04:11:55 2009 +0000
Modified BamAlignment data members to match BAM specs (signed vs unsigned ints)
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@28 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 655263adb43685cb53d84447a0c72f550df764a0
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Sep 30 16:55:07 2009 +0000
changed SIZEOF_INT to BT_SIZEOF_INT - namespace collision on Xcode-GCC
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@27 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 5255969ee7c62eb6f08365ff5ddd5dc90498c3ce
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Sep 25 17:59:46 2009 +0000
Changed BamAlignment::InsertSize to signed int... need to test
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@26 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit e76a6e48a2b596c697783cc2525ea85c61d5e4cd
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Sep 17 22:02:24 2009 +0000
Changed BGZF data member to pointer... to force buffer clean out with new/delete on reader open/close
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@25 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit d5fd4c06004e923f00048d2d32a3dbbbf29033b5
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue Aug 4 20:44:19 2009 +0000
fixed a bug where the terminal null wasn't being saved in SaveAlignment.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@24 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit ac62e75e098e999270f7f23e085504271a81de9d
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Jul 16 15:08:20 2009 +0000
Changed BAM_CORE_SIZE to unsigned int to remove signed comparison warning in BamReader.cpp:543
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@23 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 9f6d489fc810c243df6d893d78c95ea113da489d
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Jul 16 15:02:14 2009 +0000
Added BamConversion back to BamTools
Updated Makefile
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@22 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 8fae52de6c4b9df3cc754554b915a886e0263d6f
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Jul 15 18:06:13 2009 +0000
Updated README
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@21 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit b81cd242cdc5eb133a21e9d63f6d933766abc994
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Wed Jul 15 18:02:28 2009 +0000
Full update to SVN after combining BamReader and BamWriter into cohesive BamTools API.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@20 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit e38ea1095fe8f77bb1fa75a1e8c13c4b904280ae
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Mon May 18 16:25:20 2009 +0000
Major overhaul of BamReader. No longer relying on bgzf.* API. Sped up random-access. STLUtilities.h no longer needed
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@19 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit ee2064d501324a290a30365518c7adf3cb56e0bb
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Apr 23 20:33:56 2009 +0000
Had signs reversed in GetOffset error check. Fixed
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@18 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 855e80b994faaf1cc12bbb62b314e4b08ef65f3d
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu Apr 23 20:26:30 2009 +0000
Removed assertion in GetOffset(), now returns -1 if regionChunks == 0. Jump() then returns false if offset = -1, else tries to Jump
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@17 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 1c5055b92d392ee9867b269105c67319a5bb522f
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sun Apr 19 20:39:29 2009 +0000
Bug fix in BamMerge.cpp by Chip
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@16 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 53d2efeb9a92d7892fc7bd4b2f62ee5779397a6a
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Mon Apr 13 15:17:17 2009 +0000
Chip - removed limits
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@15 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit bcddc83db58c2da241c1e81be260609cdbe36bc6
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Mon Apr 13 13:45:48 2009 +0000
Added Chip's BamMerge to the repository
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@14 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit a7ada45ca6f4761f5c03fe6a0bf90afd142dd14b
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sat Apr 11 03:45:55 2009 +0000
Fixed some of the output for tag data.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@13 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit c41bbc59762754bb3267188cbb4a3801a4eecf9f
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sat Apr 11 03:45:39 2009 +0000
Forgot some include statements.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@12 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit ccc66728ab56d429c3b3e72c261a3cefc143d197
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sat Apr 11 03:32:53 2009 +0000
Added tag data support.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@11 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 6b82ce9b307efea5b6c26d5a534bdb4a47c8a10e
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sat Apr 11 03:31:59 2009 +0000
Added support for the tag data and provided a GetReadGroup accessor.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@10 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 17287619e3f072eaffb41304ec011f747f215005
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Sat Apr 11 01:25:31 2009 +0000
removed DOS line endings
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@9 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit aae68c7e5b5780eb984f11c287f03b5684635843
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 18:03:14 2009 +0000
Removed the profiling options since they shouldn't be standard.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@8 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 70251e6562b4747db989c92d87359df069cf4dc6
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 18:00:26 2009 +0000
Made many improvements to the code that pass the stricter syntax checking in Visual Studio.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@7 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 3770d40026b4af9725a573c61c8a67204562ca2c
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 17:59:34 2009 +0000
Updated the header text to give credit to the Broad Institute for the bgzf routines.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@6 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit de3817f963a3ed45cc084414b2af078962010b61
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 17:59:00 2009 +0000
Defined some of the non-standard data types for compatibility with Visual Studio.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@5 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit ff8f647fbdab9758b3c91fd984199568d1ecd2e1
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 16:06:39 2009 +0000
Added BamConversion to the make clean command
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@4 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit be515600bf37c68d864d2dbe25726c632e727fa9
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 15:26:37 2009 +0000
Updated BamReaderMain.cpp to remove unused variable warnings from compile.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@3 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 3ba4b5eb3f88fd8f24af8bf83ba218b84faa87ba
Author: mikaels <mikaels at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 15:07:49 2009 +0000
Initial import.
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@2 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
commit 9adc6b6b950ac023bac1d21905129a2b6e8659f1
Author: barnett <barnett at 9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri Apr 10 15:06:28 2009 +0000
creating directories
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@1 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
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