| HEAD | eb8c75d | Updated the README. | 26 May 2017, 00:22:05 UTC |
| refs/heads/adapter-test | b185d93 | code refactored | 30 July 2019, 09:48:33 UTC |
| refs/heads/alpha | fe272f9 | Updated the README. | 28 February 2017, 19:26:07 UTC |
| refs/heads/bugfix | 5f4733a | Updated the program version and the README. | 25 May 2017, 22:54:22 UTC |
| refs/heads/cleanup | 436edc0 | Removed an empty file. | 05 January 2016, 13:06:30 UTC |
| refs/heads/dev | c03006e | Merge branch 'master' into dev | 01 March 2017, 10:52:09 UTC |
| refs/heads/devhash | a4d54a6 | Fixed the mapping quality calculation. Ambiguity is now calculated with respect to the number of covered bases instead of the number of kmers. The parsimonious mode is now switched off by default, use --parsim to switch it on. For parsimonious mode, I removed the 0.50f for the minimum bin value - this is now only determined with the --min-bin-perc parameter. Bin value is calculated by summing the counts for the current bin, and half the counts of a bin before and a bin after. | 30 March 2016, 15:23:36 UTC |
| refs/heads/exon-extending | 581b858 | Local alignment improvements | 08 November 2018, 16:16:21 UTC |
| refs/heads/extanchorend | 2e314e6 | Fixed a bug introduced in this branch. The beginning of the read could have gotten unaligned by accident. | 09 April 2016, 19:19:16 UTC |
| refs/heads/fixedseed | cf75277 | This version uses only full seeds of 13 bases. | 14 September 2015, 09:26:14 UTC |
| refs/heads/index | 25f1eeb | Updated the README and the changelog. | 05 March 2017, 00:03:48 UTC |
| refs/heads/master | eb8c75d | Updated the README. | 26 May 2017, 00:22:05 UTC |
| refs/heads/noL1 | 24dd87f | This version uses default gapped spaced seeds (both of them), but does not use L1 filtering in the default mode. | 14 September 2015, 11:19:30 UTC |
| refs/heads/noLCSkButWithL1 | ac490e2 | This version uses default gapped spaced seeds (both of them), but does not use LCSk calculation. However, L1 linear regression is used to estimate the frame of the mapping location for semiglobal alignment. | 14 September 2015, 11:32:55 UTC |
| refs/heads/noLCSkL1 | dac543e | Fixed a bug in the last commit, two important lines were accidentally commented. | 14 September 2015, 11:34:21 UTC |
| refs/heads/onlyseed41414 | 378c379 | This version uses gapped spaced seed, but only the shape 4-1-4-1-4. | 14 September 2015, 09:40:03 UTC |
| refs/heads/onlyseed616 | afd570e | This version uses gapped spaced seed, but only the shape 6-1-6. | 14 September 2015, 09:35:29 UTC |
| refs/heads/owler | 9f8c818 | In development, from around 18.09.2016. Not sure if it's stable. | 10 November 2016, 10:36:17 UTC |
| refs/heads/rna | 8667a9b | Merge branch 'rna' of https://github.com/isovic/graphmap into rna | 01 March 2017, 23:23:49 UTC |
| refs/heads/rna-alpha | ede6725 | Process read refactored | 13 January 2019, 12:00:00 UTC |
| refs/heads/rna-dev | 581b858 | Local alignment improvements | 08 November 2018, 16:16:21 UTC |
| refs/heads/test-instance | 06493fd | removed realigning for testing purposes | 19 December 2018, 16:34:32 UTC |
| refs/heads/trans | e55a18c | v0.4.0 -> v0.4.1 | 27 January 2017, 23:52:18 UTC |
| refs/tags/0.22 | 83c6457 | Updated the README. | 12 November 2015, 18:11:02 UTC |
| refs/tags/0.22.1 | db1362c | Fixed issues with overhanging bases when aligning near a gap while using anchored alignment. The first issue was that the incremental hash key should have been reset when an unknown base was met, because it couldn't be 2bitpacked. The other one was that SeqAn, unlike EDlib, reports alignments even if all bases are Xs. I placed a threshold on the edit distance on alignment of the front and back part of a read (before first and after last alignment). These parts should not have edit distance larger than half their length. Otherwise, the read will be clipped on that end. | 16 November 2015, 00:52:31 UTC |
| refs/tags/v0.21 | 4d04c1b | Recompiled. | 09 July 2015, 20:38:34 UTC |
| refs/tags/v0.3.0 | 7f23b69 | Attempting to merge with master. | 15 April 2016, 12:10:52 UTC |
