https://github.com/sfu-compbio/mrsfast

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Revision Author Date Message Commit Date
cf8e678 Update Makefile 10 June 2020, 20:07:02 UTC
659bdf1 Merge pull request #10 from f0t1h/master Fixes the problem where there is a tab after the contig name 10 June 2020, 18:41:50 UTC
cbe04b9 Fixes the problem where there is a tab after the contig name 10 June 2020, 18:38:02 UTC
75b4930 Update README.md 13 November 2019, 07:26:14 UTC
7a479e8 Merge pull request #9 from baraaorabi/patch-2 Update README.md 11 September 2019, 02:37:20 UTC
be43d64 Update README.md 10 September 2019, 18:00:05 UTC
6c8a15b Merge pull request #8 from baraaorabi/patch-1 Allowing for dynamic CC variable 06 September 2019, 20:20:33 UTC
87ad26e Allowing for dynamic CC variable 06 September 2019, 18:53:57 UTC
32dda6a Update README.md tail crop description. 16 November 2016, 22:28:51 UTC
7c56e31 --tail-crop option added. 16 November 2016, 22:24:59 UTC
47fe86a Changing the version number to 3.3.11 30 August 2016, 18:00:51 UTC
92befe5 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 Bug Fix: Fixing MPOS in second mate of limited mapping mode. 12 August 2016, 08:13:10 UTC
f582f7c 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 Merge pull request #1 from bnelsj/master Added exit() if no reads are found for mapping 19 October 2015, 21:46:08 UTC
02e7fa2 Added exit() if no reads are found for mapping 09 October 2015, 17:41:15 UTC
e2f75ff Merge branch 'master' of https://github.com/sfu-compbio/mrsfast 17 September 2015, 19:13:16 UTC
9c81e81 Version info updated 17 September 2015, 18:53:27 UTC
5bcc2ae Merge branch 'dev' 17 September 2015, 18:46:46 UTC
663bc05 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 Update README.md 12 June 2015, 22:09:06 UTC
f380a5b Updated README.md 12 June 2015, 19:55:29 UTC
85704b9 Updating README.md file 10 June 2015, 05:00:07 UTC
5c68da9 Version info updated 17 March 2015, 22:26:27 UTC
fc1ddcc Merge branch 'dev' 17 March 2015, 22:23:07 UTC
262512d Makefile supports the multi-thread option -j 17 March 2015, 21:40:01 UTC
8b98d77 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 Version info updated 03 November 2014, 22:46:56 UTC
d9ec85a 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 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 Version info updated 23 September 2014, 19:50:35 UTC
9cba1cb Merge branch 'dev' Merge for version 3.3.4 release 23 September 2014, 19:38:27 UTC
281835c Maximum number of SNPs increased to 6 million per chromosome 23 September 2014, 19:36:20 UTC
15daaae Bug fix: Output buffer overflow in single best-mapping mode 15 September 2014, 19:13:34 UTC
1a9dbb2 Merge branch 'dev' 12 September 2014, 18:10:38 UTC
1caa330 Bug fix: snp_indexer crashed when path did not exist. New version 3.3.3 12 September 2014, 18:05:58 UTC
2c637a0 Bug fix: Crashed in paired-end SNP mode when reads are chunked 11 August 2014, 19:12:39 UTC
f47ff33 README.md edited online with Bitbucket 06 August 2014, 21:49:44 UTC
755e294 Version info updated 06 August 2014, 21:36:35 UTC
51ccaac Merge branch 'dev' 06 August 2014, 21:35:35 UTC
83cbd11 README.md edited online with Bitbucket 06 August 2014, 21:32:05 UTC
ad495cc README.md edited online with Bitbucket 06 August 2014, 21:30:58 UTC
b3187d4 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 Bug fix: Paired-end best mapping crashed 06 August 2014, 00:36:13 UTC
587f957 Bug fix: wrong fclose when input is compressed paired-end 05 August 2014, 23:42:17 UTC
45efa5b Safety measures for -n option 05 May 2014, 22:55:18 UTC
80e9c53 Updating the release information. 31 March 2014, 08:25:32 UTC
538dcfa Merge branch 'dev' 31 March 2014, 08:14:16 UTC
504b5e9 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 .sam is now optional at the end of output file (-o option) 08 March 2014, 01:22:40 UTC
ad2c511 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 with-sse4 option added to makefile 31 January 2014, 22:28:07 UTC
8dea2bf Updating Changelog to reflect the release changes 15 January 2014, 06:51:58 UTC
190712b Merge from Dev to Master 14 January 2014, 09:22:11 UTC
7c87f8b Version 3.3.0. Ported to OS X and compatible with clang 14 January 2014, 08:48:53 UTC
58c418f Bug fix: Q-gram count was not calculated for the last character of the reference genome 03 October 2013, 20:30:30 UTC
eeef3fd fixing typos in man page 13 September 2013, 22:42:29 UTC
6ac903a SNPIndexer.o is now deleted after make 13 September 2013, 22:08:21 UTC
10a1021 Version updated to 3.2.0. Small bug in best paired-end fixed 13 September 2013, 21:13:18 UTC
cc7d917 Updated help file 12 September 2013, 04:08:47 UTC
ffaf252 -q option changed to --snp-qual. Help file changed accordingly 12 September 2013, 01:13:30 UTC
ed9f532 -q option added. Help file updated accordingly 05 September 2013, 06:21:50 UTC
c4dc3eb Bug Fix: calculateMD_SNP debugged 14 August 2013, 23:35:49 UTC
945c308 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 Installation and Examples segments added to the help page 24 July 2013, 10:14:17 UTC
d53b6c3 -o /dev/null is OK to use 24 July 2013, 04:37:56 UTC
85a02e0 Fixed Makefile for SSE4 and gcc version 24 July 2013, 00:01:52 UTC
43923aa Changelog for 2.6.0.4 is update. 23 July 2013, 22:57:58 UTC
d4eb8b7 Patch sent by Jamie.K Teer on gzip PE input 23 July 2013, 22:51:33 UTC
beb96b9 All functions use buffered output 23 July 2013, 02:10:55 UTC
aabf446 Mrsfast edit 18 July 2013, 23:26:39 UTC
32c05ca Mrsfast improvements 18 July 2013, 23:25:23 UTC
48e113a Improved Hashtable threading 18 July 2013, 23:09:01 UTC
683bed5 Improving IO for reads 18 July 2013, 23:07:17 UTC
7730e64 Updating the version number 10 July 2013, 20:38:20 UTC
e70118f Fixed the bug with SSE4 definitions 18 May 2013, 00:40:21 UTC
da42f2b New Makefile with new targets debug and profile 18 May 2013, 00:14:58 UTC
8373831 Best mapping pruning added. disable-sam-header and max-discordant options renamed. 17 May 2013, 20:35:34 UTC
48934e6 Updating the HELP file to a new man format 17 May 2013, 19:53:55 UTC
2451d95 Merge branch 'dev' of bitbucket.org:compbio/mrsfast into dev 16 May 2013, 22:56:46 UTC
ec22630 Checksum length extended 16 May 2013, 22:56:05 UTC
6aa8bb7 Bug Fix: Quality not reversed in single best mode 16 May 2013, 22:07:04 UTC
39958d0 Simpler implementation of no-sam-header option 16 May 2013, 00:08:33 UTC
d4277a3 no-sam-header option added 15 May 2013, 23:39:00 UTC
7fc1074 Extra reverseComplement() removed from preProcessReads(). Checksum type parametrized 14 May 2013, 02:12:22 UTC
bd2cee1 Few extra instructions removed from verifySeq() 14 May 2013, 00:44:40 UTC
a281407 Extra 'if' removed from verifySeq 01 May 2013, 19:46:07 UTC
c261fdc Little time improvement for read loading 26 April 2013, 23:47:28 UTC
d3d9b53 Bug fix: -n option crashed when chunking 24 April 2013, 20:27:05 UTC
feef13a Discordant mode: mates mapped to the same location are reported with type - 23 April 2013, 23:34:21 UTC
a95c1b0 Merge branch 'dev' of bitbucket.org:compbio/mrsfast into dev 18 April 2013, 00:43:04 UTC
b98ee6f Discordant mode chunking problem fixed. Discordant cutoff option added. 18 April 2013, 00:34:12 UTC
a28167d disable-nohits option added 22 March 2013, 19:19:18 UTC
0304aee Little fix for SEQ_LEN calculation 11 March 2013, 21:03:17 UTC
0cdf3e5 BUG FIX: Possible negative value for minPairedEndDistance fixed. 22 January 2013, 07:14:49 UTC
d56d572 BUG FIX: gz input for second file fixed. lib output fixed. 22 January 2013, 02:50:49 UTC
3aa9df0 Fixes for the last update 21 January 2013, 23:32:47 UTC
be64a79 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 Bug fix: little fix for crop option 27 November 2012, 23:25:35 UTC
1cb0fdb Removed version from source files. Added support for sse4 on machines that had no sse4 instructions 27 November 2012, 01:50:42 UTC
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