| 1b76bf6 | Sergey Koren | 19 May 2021, 17:21:41 UTC | Merge pull request #130 from EdHarry/patch-1 Fix layout_unitigs | 19 May 2021, 17:21:41 UTC |
| 4c80ac1 | Jay Ghurye | 13 May 2021, 11:04:20 UTC | Merge pull request #139 from c-zhou/master fix bugs | 13 May 2021, 11:04:20 UTC |
| e407e61 | Chenxi Zhou | 10 May 2021, 09:11:27 UTC | fix bugs related to converting alignment coordinates on contigs to those on scaffolds and bugs related to counting REs on scaffolds | 10 May 2021, 09:11:27 UTC |
| e6e3c77 | Ed Harry | 29 March 2021, 12:21:41 UTC | Fix layout_unitigs Shouldn't this code block look like this? | 29 March 2021, 12:21:41 UTC |
| 8b1e2dc | Jay Ghurye | 28 March 2021, 02:48:16 UTC | Merge pull request #113 from feedmewifi/patch-1 corrected spelling mistake in README.md | 28 March 2021, 02:48:16 UTC |
| aa4f1bf | Jay Ghurye | 28 March 2021, 02:48:02 UTC | Merge pull request #115 from VarIr/shebang add Python2 shebang | 28 March 2021, 02:48:02 UTC |
| c297934 | Jay Ghurye | 28 March 2021, 02:47:30 UTC | Merge pull request #126 from stajichlab/stajichlab_UCR_fixes Fixes for python2 forcing, remove complier warnings, fix cmdline problem in break_contigs in run_pipeline | 28 March 2021, 02:47:30 UTC |
| c21871b | Jason Stajich | 15 January 2021, 04:13:43 UTC | change execute bit | 15 January 2021, 04:13:43 UTC |
| c6b537b | Jason Stajich | 15 January 2021, 04:13:32 UTC | fix C++ code to remove warnings for unsigned and unused variables | 15 January 2021, 04:13:32 UTC |
| 4a35b56 | Jason Stajich | 14 January 2021, 23:05:38 UTC | the min-length cutoff for the scaffolds parameter needs to be in before the redirect | 14 January 2021, 23:05:38 UTC |
| 856f26c | Jason Stajich | 14 January 2021, 23:03:13 UTC | force python2 for all scripts and steps | 14 January 2021, 23:03:13 UTC |
| 216bb63 | Roman Feldbauer | 05 November 2020, 17:37:36 UTC | add Python2 shebang Allow running Salsa script as command, ensuring python2 | 05 November 2020, 17:37:36 UTC |
| c6e1dd0 | feedmewifi | 02 November 2020, 20:21:38 UTC | corrected spelling mistake in README.md | 02 November 2020, 20:21:38 UTC |
| 974589f | Jay Ghurye | 01 October 2019, 17:51:40 UTC | prints warning if not enough links are present, instead of terminating | 01 October 2019, 17:51:40 UTC |
| 22d5382 | Sergey Koren | 22 August 2019, 20:47:34 UTC | Check both for file exists and non-empty Add check for ':' in fasta (#20), clarify docs to specify ':' cannot be in the fasta records | 22 August 2019, 20:47:34 UTC |
| f9cfff7 | Sergey Koren | 22 August 2019, 20:21:33 UTC | Add check for proper restriction sites, update README | 22 August 2019, 20:21:33 UTC |
| 8296b28 | Jay Ghurye | 08 July 2019, 14:24:26 UTC | Merge pull request #78 from arangrhie/patch-1 add the missing `/` | 08 July 2019, 14:24:26 UTC |
| 2c5fcea | Arang Rhie | 08 July 2019, 14:19:50 UTC | add the missing `/` | 08 July 2019, 14:19:50 UTC |
| e6d70b3 | Jay Ghurye | 04 June 2019, 19:14:26 UTC | Merge pull request #74 from pickettbd/master added write permissions to scaffold_length_iteration_1 after copying from lengths file | 04 June 2019, 19:14:26 UTC |
| 1789762 | Brandon Pickett | 04 June 2019, 14:30:16 UTC | added write permissions to scaffold_length_iteration_1 after copying from lengths file | 04 June 2019, 14:30:16 UTC |
| 02018dc | Jay Ghurye | 29 May 2019, 15:07:39 UTC | Update README.md | 29 May 2019, 15:07:39 UTC |
| 5b50f2e | Jay Ghurye | 29 May 2019, 15:06:10 UTC | DNAse support added | 29 May 2019, 15:06:10 UTC |
| 67fe937 | Jay Ghurye | 14 March 2019, 02:00:55 UTC | Update README.md | 14 March 2019, 02:00:55 UTC |
| 14c1327 | Jay Ghurye | 14 March 2019, 02:00:19 UTC | Update README.md | 14 March 2019, 02:00:19 UTC |
| 1b4bdf1 | machinegun | 14 March 2019, 01:01:58 UTC | Merge branch 'master' of ssh://github.com/machinegun/SALSA | 14 March 2019, 01:01:58 UTC |
| ce04802 | machinegun | 14 March 2019, 01:01:44 UTC | support to convert salsa output to .hic added | 14 March 2019, 01:01:44 UTC |
| 68a65b4 | Jay Ghurye | 29 October 2018, 01:46:04 UTC | Update layout_unitigs.py | 29 October 2018, 01:46:04 UTC |
| e729193 | machinegun | 25 October 2018, 13:54:04 UTC | stringency reduced | 25 October 2018, 13:54:04 UTC |
| 379428d | machinegun | 22 October 2018, 20:40:40 UTC | layout_unitigs.py | 22 October 2018, 20:40:40 UTC |
| 2e85a1f | machinegun | 16 October 2018, 16:03:39 UTC | Merge branch 'master' of ssh://github.com/machinegun/SALSA | 16 October 2018, 16:03:39 UTC |
| 0b7f696 | machinegun | 16 October 2018, 16:03:30 UTC | end size increased | 16 October 2018, 16:03:30 UTC |
| 0d8ecb0 | Jay Ghurye | 26 September 2018, 04:59:19 UTC | Update README.md | 26 September 2018, 04:59:19 UTC |
| a462ad6 | machinegun | 25 September 2018, 13:38:18 UTC | stitching bug fix | 25 September 2018, 13:38:18 UTC |
| e1de2b7 | machinegun | 19 September 2018, 15:03:22 UTC | non-existent nodes bug removed | 19 September 2018, 15:03:22 UTC |
| dd4fce8 | machinegun | 19 September 2018, 14:08:07 UTC | RE site updating bug removed | 19 September 2018, 14:08:07 UTC |
| cae1054 | machinegun | 26 August 2018, 20:57:25 UTC | id bug removed | 26 August 2018, 20:57:25 UTC |
| 7fa846d | machinegun | 26 August 2018, 17:08:44 UTC | contig and misjoin breaking improved to consider adptive cutoffs for pairto consider | 26 August 2018, 17:08:44 UTC |
| c950450 | machinegun | 25 August 2018, 20:22:14 UTC | Merge branch 'master' of ssh://github.com/machinegun/SALSA | 25 August 2018, 20:22:14 UTC |
| d541ad9 | machinegun | 25 August 2018, 20:21:38 UTC | sequences output in decreasing length order | 25 August 2018, 20:21:38 UTC |
| 7e99530 | Jay Ghurye | 19 May 2018, 20:45:19 UTC | Update README.md | 19 May 2018, 20:45:19 UTC |
| 9d672e7 | machinegun | 13 April 2018, 04:14:34 UTC | option added to filter the bed file | 13 April 2018, 04:14:34 UTC |
| 0f2181d | machinegun | 10 April 2018, 13:10:51 UTC | printing bug removed | 10 April 2018, 13:10:51 UTC |
| bc29ba3 | machinegun | 28 February 2018, 14:38:36 UTC | name mapping bug removed | 28 February 2018, 14:38:36 UTC |
| 8b326cc | Jay Ghurye | 14 February 2018, 19:18:56 UTC | Update README.md | 14 February 2018, 19:18:56 UTC |
| 4aad289 | machinegun | 14 February 2018, 15:02:53 UTC | id names from original assembly preserved | 14 February 2018, 15:02:53 UTC |
| 366e2b0 | machinegun | 10 February 2018, 15:27:54 UTC | Merge branch 'master' of ssh://github.com/machinegun/SALSA | 10 February 2018, 15:27:54 UTC |
| eb9aeec | machinegun | 10 February 2018, 15:27:44 UTC | join validation code updated | 10 February 2018, 15:27:44 UTC |
| cc6cd7f | Jay Ghurye | 30 January 2018, 02:07:44 UTC | Create LICENSE | 30 January 2018, 02:07:44 UTC |
| f491d66 | machinegun | 28 January 2018, 06:23:10 UTC | indexing bug removed | 28 January 2018, 06:23:10 UTC |
| 72f84d5 | machinegun | 12 January 2018, 18:05:21 UTC | breaking cutoff reduced | 12 January 2018, 18:05:21 UTC |
| 2836d0e | machinegun | 12 January 2018, 05:11:03 UTC | Merge branch 'master' of ssh://github.com/machinegun/SALSA | 12 January 2018, 05:11:03 UTC |
| 0f08f83 | machinegun | 12 January 2018, 05:10:23 UTC | graph bug removed | 12 January 2018, 05:10:23 UTC |
| 863203d | Jay Ghurye | 12 December 2017, 16:21:01 UTC | Update README.md | 12 December 2017, 16:21:01 UTC |
| 13e0613 | Jay Ghurye | 29 November 2017, 20:53:14 UTC | Update README.md | 29 November 2017, 20:53:14 UTC |
| 55cd136 | machinegun | 22 November 2017, 16:53:23 UTC | readme updated | 22 November 2017, 16:53:23 UTC |
| e7f8d97 | machinegun | 22 November 2017, 16:48:57 UTC | option added to output scaffolds at each iteration | 22 November 2017, 16:48:57 UTC |
| 3d7a032 | Mr Jay Shrirang Ghurye | 21 November 2017, 21:28:36 UTC | some description added | 21 November 2017, 21:28:36 UTC |
| 4313e57 | Mr Jay Shrirang Ghurye | 21 November 2017, 21:16:22 UTC | some description added | 21 November 2017, 21:16:22 UTC |
| 47938f2 | Mr Jay Shrirang Ghurye | 21 November 2017, 21:09:37 UTC | some description added | 21 November 2017, 21:09:37 UTC |
| 3df5ab9 | Jay Ghurye | 21 November 2017, 20:38:58 UTC | Update README.md | 21 November 2017, 20:38:58 UTC |
| 7744297 | Mr Jay Shrirang Ghurye | 21 November 2017, 20:38:10 UTC | readme updated | 21 November 2017, 20:38:10 UTC |
| 4b0753b | Mr Jay Shrirang Ghurye | 21 November 2017, 20:29:51 UTC | readmed updated | 21 November 2017, 20:29:51 UTC |
| ca07645 | Mr Jay Shrirang Ghurye | 21 November 2017, 20:22:52 UTC | README updated | 21 November 2017, 20:22:52 UTC |
| b4993ad | Mr Jay Shrirang Ghurye | 21 November 2017, 20:20:40 UTC | readme updated | 21 November 2017, 20:20:40 UTC |
| 9376920 | Mr Jay Shrirang Ghurye | 21 November 2017, 20:15:44 UTC | made new salsa on master | 21 November 2017, 20:15:44 UTC |
| 996622f | Jay Ghurye | 21 November 2017, 19:56:40 UTC | Create README.md | 21 November 2017, 19:56:40 UTC |
| 3d11b38 | Mr Jay Shrirang Ghurye | 21 November 2017, 19:53:48 UTC | exit status changed | 21 November 2017, 19:53:48 UTC |
| f1f98bd | Mr Jay Shrirang Ghurye | 21 November 2017, 19:52:07 UTC | Makefile added | 21 November 2017, 19:52:07 UTC |
| 96a3e23 | Mr Jay Shrirang Ghurye | 21 November 2017, 19:39:42 UTC | first commit of the updated code | 21 November 2017, 19:39:42 UTC |
| 833fb11 | Jay Ghurye | 09 November 2017, 20:56:43 UTC | Update README.md | 09 November 2017, 20:56:43 UTC |
| f790e48 | Jay Ghurye | 09 October 2017, 19:22:37 UTC | Create LICENSE | 09 October 2017, 19:22:37 UTC |
| f49f4d6 | Jay Ghurye | 01 September 2017, 22:54:54 UTC | Update README.md | 01 September 2017, 22:54:54 UTC |
| 31d4f95 | Jay Ghurye | 09 June 2017, 13:52:44 UTC | Merge pull request #11 from godotgildor/patch-1 Create break_contigs.cpp | 09 June 2017, 13:52:44 UTC |
| 53330ef | Brett T. Hannigan | 09 June 2017, 06:59:10 UTC | Create break_contigs.cpp Modify the code so that the first record referencing a given contig is also included in the list. The previous code simply created the empty vector of records for the new contig but did not place the record in that vector. | 09 June 2017, 06:59:10 UTC |
| 28f7545 | Jay Ghurye | 23 February 2017, 20:00:08 UTC | Update README.md | 23 February 2017, 20:00:08 UTC |
| 480cda2 | tester | 15 November 2016, 03:24:06 UTC | added n to revcompl | 15 November 2016, 03:24:06 UTC |
| 759af74 | Jay Ghurye | 28 October 2016, 04:23:17 UTC | tab issue in run.py removed | 28 October 2016, 04:23:17 UTC |
| 69ef514 | Jay Ghurye | 09 October 2016, 20:07:39 UTC | str bug from run.py removed | 09 October 2016, 20:07:39 UTC |
| cccef1e | Jay Ghurye | 07 October 2016, 15:31:12 UTC | string to int conversion added | 07 October 2016, 15:31:12 UTC |
| db71d97 | Jay Ghurye | 06 October 2016, 19:42:40 UTC | length cutoff added | 06 October 2016, 19:42:40 UTC |
| 5abd990 | Jay Ghurye | 30 September 2016, 16:06:43 UTC | changed flag for bed file | 30 September 2016, 16:06:43 UTC |
| f9022b0 | Jay Ghurye | 30 September 2016, 16:05:34 UTC | changed create links to new links for faster result | 30 September 2016, 16:05:34 UTC |
| 2970678 | Jay Ghurye | 25 September 2016, 02:46:20 UTC | minor error removed | 25 September 2016, 02:46:20 UTC |
| e728bb7 | Jay Ghurye | 23 September 2016, 22:35:02 UTC | agp file added in output directory | 23 September 2016, 22:35:02 UTC |
| e184fff | tester | 23 September 2016, 18:11:27 UTC | Merge pull request #5 from skoren/master Add path to script directory, skip done steps | 23 September 2016, 18:11:27 UTC |
| a4ddc5e | Sergey Koren | 23 September 2016, 18:06:34 UTC | Add path to script directory for sub-programs so they don't have to be in the path, skip steps if output already exists, add force option to clean up | 23 September 2016, 18:06:34 UTC |
| 1d67120 | tester | 21 September 2016, 18:28:45 UTC | Merge pull request #4 from zeeev/master tab issue | 21 September 2016, 18:28:45 UTC |
| cda9d74 | Zev N. Kronenberg | 21 September 2016, 18:25:41 UTC | tab was off, throwing an error | 21 September 2016, 18:25:41 UTC |
| d0f5341 | Jay Ghurye | 11 September 2016, 19:33:28 UTC | made reverse complement generalized | 11 September 2016, 19:33:28 UTC |
| 95810d0 | Jay Ghurye | 11 September 2016, 19:16:39 UTC | print removed | 11 September 2016, 19:16:39 UTC |
| 21a1879 | Jay Ghurye | 11 September 2016, 18:01:16 UTC | biopython dependency removed | 11 September 2016, 18:01:16 UTC |
| 80f2555 | Jay Ghurye | 24 August 2016, 08:30:11 UTC | made reverse complement general | 24 August 2016, 08:30:11 UTC |
| fba668a | Jay Ghurye | 23 August 2016, 10:14:37 UTC | Merge branch 'master' of https://github.com/machinegun/hi-c-scaffold | 23 August 2016, 10:14:37 UTC |
| 75ff5ac | Jay Ghurye | 23 August 2016, 10:14:24 UTC | changed IO from biopython to pbcore | 23 August 2016, 10:14:24 UTC |
| 13656d7 | tester | 23 August 2016, 10:09:07 UTC | Update run.py | 23 August 2016, 10:09:07 UTC |
| e20d3ea | Jay Ghurye | 20 August 2016, 23:50:37 UTC | makefile error fixed | 20 August 2016, 23:50:37 UTC |
| 07cea5d | tester | 20 August 2016, 23:45:39 UTC | Delete Makefile | 20 August 2016, 23:45:39 UTC |
| 313947a | tester | 19 August 2016, 18:31:09 UTC | Delete links_to_graph2.py | 19 August 2016, 18:31:09 UTC |
| af82710 | tester | 19 August 2016, 18:30:53 UTC | Delete run.sh | 19 August 2016, 18:30:53 UTC |
| 4bc8923 | tester | 19 August 2016, 18:29:37 UTC | Add files via upload | 19 August 2016, 18:29:37 UTC |
