6c8a15b | Faraz Hach | 06 September 2019, 20:20:33 UTC | Merge pull request #8 from baraaorabi/patch-1 Allowing for dynamic CC variable | 06 September 2019, 20:20:33 UTC |
87ad26e | Baraa Orabi /baraːʔ ʕraːbi/ | 06 September 2019, 18:53:57 UTC | Allowing for dynamic CC variable | 06 September 2019, 18:53:57 UTC |
32dda6a | Faraz Hach | 16 November 2016, 22:28:51 UTC | Update README.md tail crop description. | 16 November 2016, 22:28:51 UTC |
7c56e31 | Faraz Hach | 16 November 2016, 22:24:59 UTC | --tail-crop option added. | 16 November 2016, 22:24:59 UTC |
47fe86a | Faraz Hach | 30 August 2016, 18:00:51 UTC | Changing the version number to 3.3.11 | 30 August 2016, 18:00:51 UTC |
92befe5 | Faraz Hach | 30 August 2016, 17:57:32 UTC | Fixing the FLAG in best mapping mode for the case in which OEA's second mate is reverse complemented. | 30 August 2016, 17:57:32 UTC |
d4b491a | Faraz Hach | 12 August 2016, 08:13:10 UTC | Bug Fix: Fixing MPOS in second mate of limited mapping mode. | 12 August 2016, 08:13:10 UTC |
f582f7c | Faraz Hach | 29 June 2016, 23:18:45 UTC | 1) exit(0) and exit(1) replaced by exit(EXIT_SUCCESS) and exit(EXIT_FAILURE), respectively 2) opening file failures are not report correct exit codes 3) concordant calculations is now reported to concordant.statistic | 29 June 2016, 23:18:45 UTC |
a3a7174 | Faraz Hach | 19 October 2015, 21:46:08 UTC | Merge pull request #1 from bnelsj/master Added exit() if no reads are found for mapping | 19 October 2015, 21:46:08 UTC |
02e7fa2 | Brad Nelson | 09 October 2015, 17:41:15 UTC | Added exit() if no reads are found for mapping | 09 October 2015, 17:41:15 UTC |
e2f75ff | Iman Sarrafi | 17 September 2015, 19:13:16 UTC | Merge branch 'master' of https://github.com/sfu-compbio/mrsfast | 17 September 2015, 19:13:16 UTC |
9c81e81 | Iman Sarrafi | 17 September 2015, 18:53:27 UTC | Version info updated | 17 September 2015, 18:53:27 UTC |
5bcc2ae | Iman Sarrafi | 17 September 2015, 18:46:46 UTC | Merge branch 'dev' | 17 September 2015, 18:46:46 UTC |
663bc05 | Iman Sarrafi | 17 September 2015, 18:36:29 UTC | 1) SNP mode is more flexible and accepts non-homosapien dbSNP (VCF) inputs. 2) Minor fix in memory allocation. 3) Typo fixed in manual. | 17 September 2015, 18:36:29 UTC |
02715ca | Iman Sarrafi | 12 June 2015, 22:09:06 UTC | Update README.md | 12 June 2015, 22:09:06 UTC |
f380a5b | Iman Sarrafi | 12 June 2015, 19:55:29 UTC | Updated README.md | 12 June 2015, 19:55:29 UTC |
85704b9 | Faraz Hach | 10 June 2015, 05:00:07 UTC | Updating README.md file | 10 June 2015, 05:00:07 UTC |
5c68da9 | Iman Sarrafi | 17 March 2015, 22:26:27 UTC | Version info updated | 17 March 2015, 22:26:27 UTC |
fc1ddcc | Iman Sarrafi | 17 March 2015, 22:23:07 UTC | Merge branch 'dev' | 17 March 2015, 22:23:07 UTC |
262512d | Iman Sarrafi | 17 March 2015, 21:40:01 UTC | Makefile supports the multi-thread option -j | 17 March 2015, 21:40:01 UTC |
8b98d77 | Iman Sarrafi | 07 January 2015, 00:21:53 UTC | 1) Bug fix: crashed in PE mode with compressed input, due to double fclose. 2) Error message is produced if --ws is specified in search mode | 07 January 2015, 00:21:53 UTC |
c40b663 | Iman Sarrafi | 03 November 2014, 22:46:56 UTC | Version info updated | 03 November 2014, 22:46:56 UTC |
d9ec85a | Iman Sarrafi | 03 November 2014, 22:42:18 UTC | 1) Bug fix: Miscalculation of number of mappings, in paired-end -n mode 2) Typo fixed in manual | 03 November 2014, 22:42:18 UTC |
6cce168 | Iman Sarrafi | 30 October 2014, 19:44:22 UTC | Bug fix: paired-end -n mode seg fault Typos fixed in manual String null pointer is set inside reverse() and reverseComplete() | 30 October 2014, 19:44:22 UTC |
6904ed5 | Iman Sarrafi | 23 September 2014, 19:50:35 UTC | Version info updated | 23 September 2014, 19:50:35 UTC |
9cba1cb | Iman Sarrafi | 23 September 2014, 19:38:27 UTC | Merge branch 'dev' Merge for version 3.3.4 release | 23 September 2014, 19:38:27 UTC |
281835c | Iman Sarrafi | 23 September 2014, 19:36:20 UTC | Maximum number of SNPs increased to 6 million per chromosome | 23 September 2014, 19:36:20 UTC |
15daaae | Iman Sarrafi | 15 September 2014, 19:13:34 UTC | Bug fix: Output buffer overflow in single best-mapping mode | 15 September 2014, 19:13:34 UTC |
1a9dbb2 | Iman Sarrafi | 12 September 2014, 18:10:38 UTC | Merge branch 'dev' | 12 September 2014, 18:10:38 UTC |
1caa330 | Iman Sarrafi | 12 September 2014, 18:05:58 UTC | Bug fix: snp_indexer crashed when path did not exist. New version 3.3.3 | 12 September 2014, 18:05:58 UTC |
2c637a0 | Iman Sarrafi | 11 August 2014, 19:12:39 UTC | Bug fix: Crashed in paired-end SNP mode when reads are chunked | 11 August 2014, 19:12:39 UTC |
f47ff33 | Iman Sarrafi | 06 August 2014, 21:49:44 UTC | README.md edited online with Bitbucket | 06 August 2014, 21:49:44 UTC |
755e294 | Iman Sarrafi | 06 August 2014, 21:36:35 UTC | Version info updated | 06 August 2014, 21:36:35 UTC |
51ccaac | Iman Sarrafi | 06 August 2014, 21:35:35 UTC | Merge branch 'dev' | 06 August 2014, 21:35:35 UTC |
83cbd11 | Iman Sarrafi | 06 August 2014, 21:32:05 UTC | README.md edited online with Bitbucket | 06 August 2014, 21:32:05 UTC |
ad495cc | Iman Sarrafi | 06 August 2014, 21:30:58 UTC | README.md edited online with Bitbucket | 06 August 2014, 21:30:58 UTC |
b3187d4 | Iman Sarrafi | 06 August 2014, 21:28:20 UTC | 1) Bug fix: Best mapping paired-end output was not convertible to BAM. 2) Bug fix: Paired-end multiple mapping crashed. 3) Manual page updated for reference to mrsFAST-Ultra paper | 06 August 2014, 21:28:20 UTC |
ba13afa | Iman Sarrafi | 06 August 2014, 00:36:13 UTC | Bug fix: Paired-end best mapping crashed | 06 August 2014, 00:36:13 UTC |
587f957 | Iman Sarrafi | 05 August 2014, 23:42:17 UTC | Bug fix: wrong fclose when input is compressed paired-end | 05 August 2014, 23:42:17 UTC |
45efa5b | Iman Sarrafi | 05 May 2014, 22:55:18 UTC | Safety measures for -n option | 05 May 2014, 22:55:18 UTC |
80e9c53 | Faraz Hach | 31 March 2014, 08:25:32 UTC | Updating the release information. | 31 March 2014, 08:25:32 UTC |
538dcfa | Iman Sarrafi | 31 March 2014, 08:14:16 UTC | Merge branch 'dev' | 31 March 2014, 08:14:16 UTC |
504b5e9 | Iman Sarrafi | 30 March 2014, 01:29:11 UTC | 1) BUG FIX: used to crash in PE discordant mode when number of chromosomes was high. Some temporary files were opened in each iteration and never closed later. This lead to failure of fopen function at some point. 2) .sam is no longer added to the output file name. This caused the output file name to be unpredictable when used in pipelines | 30 March 2014, 01:29:11 UTC |
4c5ae0e | Iman Sarrafi | 08 March 2014, 01:22:40 UTC | .sam is now optional at the end of output file (-o option) | 08 March 2014, 01:22:40 UTC |
ad2c511 | Iman Sarrafi | 19 February 2014, 00:26:38 UTC | Bug fix: In discordant mode with interleaved reads program crashed before finishing. It didn't affect the output though. | 19 February 2014, 00:26:38 UTC |
f1dd45c | Iman Sarrafi | 31 January 2014, 22:28:07 UTC | with-sse4 option added to makefile | 31 January 2014, 22:28:07 UTC |
8dea2bf | Faraz Hach | 15 January 2014, 06:51:58 UTC | Updating Changelog to reflect the release changes | 15 January 2014, 06:51:58 UTC |
190712b | Faraz Hach | 14 January 2014, 09:22:11 UTC | Merge from Dev to Master | 14 January 2014, 09:22:11 UTC |
7c87f8b | Faraz Hach | 14 January 2014, 08:48:53 UTC | Version 3.3.0. Ported to OS X and compatible with clang | 14 January 2014, 08:48:53 UTC |
58c418f | Iman Sarrafi | 03 October 2013, 20:30:30 UTC | Bug fix: Q-gram count was not calculated for the last character of the reference genome | 03 October 2013, 20:30:30 UTC |
eeef3fd | Faraz Hach | 13 September 2013, 22:42:29 UTC | fixing typos in man page | 13 September 2013, 22:42:29 UTC |
6ac903a | Iman Sarrafi | 13 September 2013, 22:08:21 UTC | SNPIndexer.o is now deleted after make | 13 September 2013, 22:08:21 UTC |
10a1021 | Iman Sarrafi | 13 September 2013, 21:13:18 UTC | Version updated to 3.2.0. Small bug in best paired-end fixed | 13 September 2013, 21:13:18 UTC |
cc7d917 | Faraz Hach | 12 September 2013, 04:08:47 UTC | Updated help file | 12 September 2013, 04:08:47 UTC |
ffaf252 | Iman Sarrafi | 12 September 2013, 01:13:30 UTC | -q option changed to --snp-qual. Help file changed accordingly | 12 September 2013, 01:13:30 UTC |
ed9f532 | Iman Sarrafi | 05 September 2013, 06:21:50 UTC | -q option added. Help file updated accordingly | 05 September 2013, 06:21:50 UTC |
c4dc3eb | Iman Sarrafi | 14 August 2013, 23:35:49 UTC | Bug Fix: calculateMD_SNP debugged | 14 August 2013, 23:35:49 UTC |
945c308 | Iman Sarrafi | 12 August 2013, 00:00:07 UTC | Improvements in SNP mode: a mismatch at a known SNP location is only ignored when the corresponding base pair quality is higher than a threshold, and also the exact alternative character (provided by dbSNP) is observed | 12 August 2013, 00:00:07 UTC |
717a24a | Iman Sarrafi | 24 July 2013, 10:14:17 UTC | Installation and Examples segments added to the help page | 24 July 2013, 10:14:17 UTC |
d53b6c3 | Iman Sarrafi | 24 July 2013, 04:37:56 UTC | -o /dev/null is OK to use | 24 July 2013, 04:37:56 UTC |
85a02e0 | Faraz Hach | 24 July 2013, 00:01:52 UTC | Fixed Makefile for SSE4 and gcc version | 24 July 2013, 00:01:52 UTC |
43923aa | Faraz Hach | 23 July 2013, 22:57:58 UTC | Changelog for 2.6.0.4 is update. | 23 July 2013, 22:57:58 UTC |
d4eb8b7 | Faraz Hach | 23 July 2013, 22:51:33 UTC | Patch sent by Jamie.K Teer on gzip PE input | 23 July 2013, 22:51:33 UTC |
beb96b9 | Iman Sarrafi | 23 July 2013, 02:10:55 UTC | All functions use buffered output | 23 July 2013, 02:10:55 UTC |
aabf446 | Faraz Hach | 18 July 2013, 23:26:39 UTC | Mrsfast edit | 18 July 2013, 23:26:39 UTC |
32c05ca | Faraz Hach | 18 July 2013, 23:25:23 UTC | Mrsfast improvements | 18 July 2013, 23:25:23 UTC |
48e113a | Faraz Hach | 18 July 2013, 23:09:01 UTC | Improved Hashtable threading | 18 July 2013, 23:09:01 UTC |
683bed5 | Faraz Hach | 18 July 2013, 23:07:17 UTC | Improving IO for reads | 18 July 2013, 23:07:17 UTC |
7730e64 | Faraz Hach | 10 July 2013, 20:38:20 UTC | Updating the version number | 10 July 2013, 20:38:20 UTC |
e70118f | Faraz Hach | 18 May 2013, 00:40:21 UTC | Fixed the bug with SSE4 definitions | 18 May 2013, 00:40:21 UTC |
da42f2b | Faraz Hach | 18 May 2013, 00:14:58 UTC | New Makefile with new targets debug and profile | 18 May 2013, 00:14:58 UTC |
8373831 | Iman Sarrafi | 17 May 2013, 20:35:34 UTC | Best mapping pruning added. disable-sam-header and max-discordant options renamed. | 17 May 2013, 20:35:34 UTC |
48934e6 | Faraz Hach | 17 May 2013, 19:53:55 UTC | Updating the HELP file to a new man format | 17 May 2013, 19:53:55 UTC |
2451d95 | Iman Sarrafi | 16 May 2013, 22:56:46 UTC | Merge branch 'dev' of bitbucket.org:compbio/mrsfast into dev | 16 May 2013, 22:56:46 UTC |
ec22630 | Iman Sarrafi | 16 May 2013, 22:56:05 UTC | Checksum length extended | 16 May 2013, 22:56:05 UTC |
6aa8bb7 | Iman Sarrafi | 16 May 2013, 22:07:04 UTC | Bug Fix: Quality not reversed in single best mode | 16 May 2013, 22:07:04 UTC |
39958d0 | Iman Sarrafi | 16 May 2013, 00:08:33 UTC | Simpler implementation of no-sam-header option | 16 May 2013, 00:08:33 UTC |
d4277a3 | Iman Sarrafi | 15 May 2013, 23:39:00 UTC | no-sam-header option added | 15 May 2013, 23:39:00 UTC |
7fc1074 | Iman Sarrafi | 14 May 2013, 02:12:22 UTC | Extra reverseComplement() removed from preProcessReads(). Checksum type parametrized | 14 May 2013, 02:12:22 UTC |
bd2cee1 | Iman Sarrafi | 14 May 2013, 00:44:40 UTC | Few extra instructions removed from verifySeq() | 14 May 2013, 00:44:40 UTC |
a281407 | Iman Sarrafi | 01 May 2013, 19:46:07 UTC | Extra 'if' removed from verifySeq | 01 May 2013, 19:46:07 UTC |
c261fdc | Iman Sarrafi | 26 April 2013, 23:47:28 UTC | Little time improvement for read loading | 26 April 2013, 23:47:28 UTC |
d3d9b53 | Iman Sarrafi | 24 April 2013, 20:27:05 UTC | Bug fix: -n option crashed when chunking | 24 April 2013, 20:27:05 UTC |
feef13a | Iman Sarrafi | 23 April 2013, 23:34:21 UTC | Discordant mode: mates mapped to the same location are reported with type - | 23 April 2013, 23:34:21 UTC |
a95c1b0 | Iman Sarrafi | 18 April 2013, 00:43:04 UTC | Merge branch 'dev' of bitbucket.org:compbio/mrsfast into dev | 18 April 2013, 00:43:04 UTC |
b98ee6f | Iman Sarrafi | 18 April 2013, 00:34:12 UTC | Discordant mode chunking problem fixed. Discordant cutoff option added. | 18 April 2013, 00:34:12 UTC |
a28167d | Iman Sarrafi | 22 March 2013, 19:19:18 UTC | disable-nohits option added | 22 March 2013, 19:19:18 UTC |
0304aee | Iman Sarrafi | 11 March 2013, 21:03:17 UTC | Little fix for SEQ_LEN calculation | 11 March 2013, 21:03:17 UTC |
0cdf3e5 | Iman Sarrafi | 22 January 2013, 07:14:49 UTC | BUG FIX: Possible negative value for minPairedEndDistance fixed. | 22 January 2013, 07:14:49 UTC |
d56d572 | Iman Sarrafi | 22 January 2013, 02:50:49 UTC | BUG FIX: gz input for second file fixed. lib output fixed. | 22 January 2013, 02:50:49 UTC |
3aa9df0 | Iman Sarrafi | 21 January 2013, 23:32:47 UTC | Fixes for the last update | 21 January 2013, 23:32:47 UTC |
be64a79 | Iman Sarrafi | 20 January 2013, 20:55:20 UTC | Output file names fixed. SNP bestMode fixed. In discordant mode sample.lib output file is created as an input for VH | 20 January 2013, 20:55:20 UTC |
97439c5 | Iman Sarrafi | 27 November 2012, 23:25:35 UTC | Bug fix: little fix for crop option | 27 November 2012, 23:25:35 UTC |
1cb0fdb | Faraz Hach | 27 November 2012, 01:50:42 UTC | Removed version from source files. Added support for sse4 on machines that had no sse4 instructions | 27 November 2012, 01:50:42 UTC |
54e115d | Iman Sarrafi | 27 November 2012, 00:59:00 UTC | SNPIndexer refactored. Makefile modified for snp_indexer | 27 November 2012, 00:59:00 UTC |
50e36a8 | Faraz Hach | 27 November 2012, 00:25:17 UTC | Adding snp_indexer to .gitignore | 27 November 2012, 00:25:17 UTC |
52b0757 | Faraz Hach | 27 November 2012, 00:24:23 UTC | snp_indexer is added to Makefile | 27 November 2012, 00:24:23 UTC |
b6037bf | Iman Sarrafi | 27 November 2012, 00:20:58 UTC | SSE4 line was commented by mistake | 27 November 2012, 00:20:58 UTC |
f6bc296 | Iman Sarrafi | 27 November 2012, 00:16:57 UTC | SNP feature updated and code refactored. SNPIndexer.c added | 27 November 2012, 00:16:57 UTC |
6d6ac04 | Iman Sarrafi | 23 November 2012, 04:55:56 UTC | Bug fix: -n option used to crash on multithread | 23 November 2012, 04:55:56 UTC |