| 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 |
| 2cad08b | Faraz Hach | 23 November 2012, 04:30:11 UTC | Changing the sort in reads and hashtable from qsort to intro sort | 23 November 2012, 04:30:11 UTC |
| 8c1a14f | Faraz Hach | 19 November 2012, 10:59:00 UTC | Adding tab per sam tools desc | 19 November 2012, 10:59:00 UTC |
| c6ab06b | Faraz Hach | 17 November 2012, 01:32:17 UTC | Add some pruning to best single-end | 17 November 2012, 01:32:17 UTC |
| cc4ee38 | Iman Sarrafi | 17 November 2012, 00:24:41 UTC | BUG FIX: used to crash when -o input was longer than 100 characters | 17 November 2012, 00:24:41 UTC |
| 68abcb9 | Faraz Hach | 16 November 2012, 02:12:46 UTC | Bug Fix: SEQ_LENGTH calculation is fixed to consider the \r\n. MAX Read Length is increased to 500 | 16 November 2012, 02:12:46 UTC |
| 0bb0142 | Faraz Hach | 15 November 2012, 06:17:56 UTC | Bug fix: Quality string end null character fixed | 15 November 2012, 06:17:56 UTC |
| 1bcbf68 | Iman Sarrafi | 10 November 2012, 04:13:25 UTC | -n option added and modified to match new changes | 10 November 2012, 04:13:25 UTC |
| b40bc14 | Faraz Hach | 10 November 2012, 00:08:09 UTC | Checksum for speed up added. Localized for reducing memory fetch. | 10 November 2012, 00:08:09 UTC |
| a492fa3 | Faraz Hach | 01 November 2012, 00:16:34 UTC | Checksum filter added. Distance Calculation updated and bug fixed. | 01 November 2012, 00:16:34 UTC |
| 295dcac | Iman Sarrafi | 23 October 2012, 22:30:38 UTC | Paired-end profiling added. (UNSTABLE) | 23 October 2012, 22:30:38 UTC |
| d26bfe5 | Iman Sarrafi | 17 October 2012, 01:21:45 UTC | New CommandLineParser.c, Little correction to SnipReader.h | 17 October 2012, 01:21:45 UTC |
| 5bdfa18 | Iman Sarrafi | 16 October 2012, 21:39:45 UTC | Snip Tolerance added. Seems to be fine, needs further testing. (UNSTABLE) | 16 October 2012, 21:39:45 UTC |
| c2bc3dd | Iman Sarrafi | 11 October 2012, 02:26:21 UTC | Read lengths are checked to be the same. checkAllReads() is added, but not used | 11 October 2012, 02:26:21 UTC |
| 4e21d14 | Iman Sarrafi | 10 October 2012, 02:21:07 UTC | Bug fix in PE bestMode. PE bestMode flags tested and debugged | 10 October 2012, 02:21:07 UTC |
| d582ba1 | Iman Sarrafi | 10 October 2012, 00:45:27 UTC | maxPairEndedDistance value set in initLoadingHashTable(), after reading maxChrLength from metaInfo | 10 October 2012, 00:45:27 UTC |
| 627efc3 | Iman Sarrafi | 09 October 2012, 22:45:53 UTC | Bug fix: In PE, in case one of the mates is discarded, the other one should still be indexed | 09 October 2012, 22:45:53 UTC |
| 86daa1c | Iman Sarrafi | 06 October 2012, 03:08:10 UTC | Bug fixes for PE best mode | 06 October 2012, 03:08:10 UTC |
| ecfe7af | Faraz Hach | 05 October 2012, 21:57:52 UTC | Merge branch 'dev' of bitbucket.org:compbio/mrsfast into dev | 05 October 2012, 21:57:52 UTC |
| 3e68886 | Faraz Hach | 05 October 2012, 21:57:41 UTC | NEW PE best mapping mode | 05 October 2012, 21:57:41 UTC |
| 8ffe353 | Iman Sarrafi | 05 October 2012, 21:13:38 UTC | output.sam and output.nohit names are fixed | 05 October 2012, 21:13:38 UTC |
| c227023 | Faraz Hach | 05 October 2012, 01:25:34 UTC | Fixing SAM headers for samtools | 05 October 2012, 01:25:34 UTC |
| 1c96b9e | Faraz Hach | 05 October 2012, 01:10:29 UTC | Bug Fix: related to indexing of the discarded reads introduced in 8a0eab3f02ad | 05 October 2012, 01:10:29 UTC |
| e38f2ea | Faraz Hach | 04 October 2012, 00:59:18 UTC | Fixing Common.h | 04 October 2012, 00:59:18 UTC |
| 91e2c42 | Iman Sarrafi | 04 October 2012, 00:48:56 UTC | Single-end best mapping mode is now using full sam specification | 04 October 2012, 00:48:56 UTC |
| 915d650 | Iman Sarrafi | 02 October 2012, 23:16:22 UTC | Paired-end crash on single read file fixed. | 02 October 2012, 23:16:22 UTC |
| dbeceaf | Iman Sarrafi | 02 October 2012, 22:31:04 UTC | initializeFAST(), initFASTChunk(), and initFASTContig() are separated. Bug fixed. | 02 October 2012, 22:31:04 UTC |
| fe441fd | Faraz Hach | 02 October 2012, 03:09:53 UTC | Fixing a bug regarding output of no hits | 02 October 2012, 03:09:53 UTC |
| 6605214 | Iman Sarrafi | 01 October 2012, 22:30:56 UTC | Paired end leak fixed | 01 October 2012, 22:30:56 UTC |
| 605cb53 | Iman Sarrafi | 25 September 2012, 00:55:04 UTC | _msf_op _msf_output _msf_optionalFields specified for each thread. Paired end bug fixed. | 25 September 2012, 00:55:04 UTC |
| e44def4 | Faraz Hach | 28 August 2012, 02:14:28 UTC | Fixed the PE mode and SAM output | 28 August 2012, 02:14:28 UTC |
| bef61b3 | Faraz Hach | 23 August 2012, 04:32:14 UTC | Memory leakage is fixed for single end mode / best single end mode. | 23 August 2012, 04:32:14 UTC |
