| HEAD | 60850dc | Disable cmake, but leave the file with a message | 16 December 2020, 10:18:06 UTC |
| refs/heads/bugfix | df9bb28 | resolve #406 The allele parser could end up in a state where we deleted alignment before their parsed alleles were removed from the list of registered alleles. Touching these could in turn cause segfaults and other undefined behavior. This commit ensures we clean up the pointers to the removed alleles correctly. | 23 August 2017, 00:43:35 UTC |
| refs/heads/build | b185873 | list bamleftalign before objects in build | 13 July 2017, 08:50:37 UTC |
| refs/heads/build-tweak | 8942eac | continue specifying dependencies | 06 January 2020, 21:21:56 UTC |
| refs/heads/building | 6a2fbdb | remove gdb flag from compilation | 07 November 2017, 19:58:09 UTC |
| refs/heads/call-on-ref-N | b5ccca1 | allow calling on N-matching bases | 01 February 2018, 12:25:19 UTC |
| refs/heads/cmakeify | 0c1b1c6 | two cores on travis | 07 January 2020, 15:56:31 UTC |
| refs/heads/cnv-map-help | fed2400 | clarify how to use the CNV map | 14 February 2019, 14:13:45 UTC |
| refs/heads/compound-haplotype | 632eb29 | resolve #437 | 14 February 2018, 11:07:31 UTC |
| refs/heads/correct-build | fae0f09 | c++11 required now | 19 December 2019, 13:58:49 UTC |
| refs/heads/coverage-limiting | 9a32a36 | minor code cleanup for clarity | 29 May 2019, 10:42:56 UTC |
| refs/heads/document-params | 133bbb7 | clarify the effect of allele exclusion filters, document best practices Also, try to document ideal use of freebayes: Run it with default parameters, *then* filter the output. | 24 August 2018, 07:52:05 UTC |
| refs/heads/error-reporting | 3346c60 | clarify that alignments mapping past the end of contigs indicates a potential problem with the input | 12 October 2017, 21:31:06 UTC |
| refs/heads/force-0-qual | 9bfee20 | force quality to be 0 when no quality string given In response to #509. | 04 June 2019, 10:13:41 UTC |
| refs/heads/gls | 13f5098 | Merge branch 'master' of github.com:ekg/freebayes into gls | 14 January 2015, 19:50:23 UTC |
| refs/heads/gvcf-chunk | 8916bd0 | add test for gVCF chunking | 15 November 2015, 18:02:01 UTC |
| refs/heads/gvcf-support | a2176b7 | add gVCF support When --gvcf is supplied, freebayes will output blocks for each region that does not have a call. These have a particular format that is not exactly the same as other records. A genotype quality is provided, but this is just the reference quality sum adjusted by the alternate quality sum. These are provided per-sample. Average depth is provided across the region. Improvement of this format is essential, and this version should stand as a placeholder for future development! | 14 November 2015, 15:16:32 UTC |
| refs/heads/haplotype-basis | a676799 | be more sensitive to variant input | 07 January 2020, 17:28:13 UTC |
| refs/heads/haplotypes | f1e6993 | remove temporary files after test | 09 July 2017, 09:28:52 UTC |
| refs/heads/long-read-optimize | f2ddf08 | avoid frequent recomputation of the alignment endposition This is expensive with long reads. | 08 October 2019, 12:12:06 UTC |
| refs/heads/master | 60850dc | Disable cmake, but leave the file with a message | 16 December 2020, 10:18:06 UTC |
| refs/heads/no-makefile | e0c0fee | update readme to indicate that the makefile is no more | 05 March 2020, 14:31:48 UTC |
| refs/heads/no-sort-alleles | 9965815 | can we get away without sorting and removing "non-unique" alleles? | 05 October 2019, 21:38:02 UTC |
| refs/heads/ploidy | 89d2312 | *actually* use SAM rather than BAM to avoid samtools version weirdness | 09 July 2017, 12:55:44 UTC |
| refs/heads/sensitive-defaults | 6725791 | match tests to current default settings | 30 March 2018, 09:10:17 UTC |
| refs/heads/skip-coverage | ffcee0d | avoid hanging in super low entropy sequence We should never be running the entropy calculation past the read end. It won't ever support a haplotype call to do so. This change may very slightly change behavior of the algorithm in low entropy sequence regions. | 03 June 2019, 13:16:34 UTC |
| refs/heads/skip-depth-partials | fbaed2e | avoid position skipping logic when getting partial alignments This isn't the right solution (we get depths over our threshold) but it will avoid segfaulting when we start throwing out alignments that push us over our depth limit. | 30 May 2019, 16:01:51 UTC |
| refs/heads/tweak-seqlib-build | 607a613 | list dependencies for seqlib | 06 January 2020, 17:02:10 UTC |
| refs/heads/unbreak-indel-input | 32bf9de | Revert "be more sensitive to variant input" This reverts commit a676799f5a64c286b3508997bd3cfe92ed4f759b. | 03 February 2020, 09:19:48 UTC |
| refs/heads/update-seqlib | 71f6837 | correct race in makefile | 06 January 2020, 14:44:46 UTC |
| refs/tags/development | 61b7bbc | use cast to get correct call to max(...) To resolve issue reported by C here: http://blog.gkno.me/post/29962850248/getting-started-with-gkno#disqus_thread | 06 December 2012, 15:15:35 UTC |
| refs/tags/first | a6caa52 | Initial Commit Drawn directly from alpha-2010-01-18. | 04 February 2010, 16:52:28 UTC |
| refs/tags/stable | b080a1e | minor fix to TRY CATCH macros Added __FILE__ name to CATCH error report. | 25 February 2010, 17:08:27 UTC |
| refs/tags/v0.1.0 | e612563 | version 0.1.0 completes prior commit, adds Version.h by default. | 13 October 2010, 22:04:11 UTC |
| refs/tags/v0.9.10 | 9755e43 | Setting Release-Version v0.9.10 | 10 December 2013, 00:24:08 UTC |
| refs/tags/v0.9.13 | dc0f063 | Merge pull request #66 from andersje/git_to_http changed git:// to https:// | 19 February 2014, 00:37:29 UTC |
| refs/tags/v0.9.14 | 698098e | Setting Release-Version v0.9.14 | 03 March 2014, 14:43:15 UTC |
| refs/tags/v0.9.15 | f0e3144 | Setting Release-Version v0.9.15 | 21 August 2014, 02:53:10 UTC |
| refs/tags/v0.9.16 | 69bf85a | Setting Release-Version v0.9.16 | 26 September 2014, 16:49:25 UTC |
| refs/tags/v0.9.17 | cb39738 | Setting Release-Version v0.9.17 | 01 October 2014, 21:20:56 UTC |
| refs/tags/v0.9.18 | 0059bdf | Setting Release-Version v0.9.18 | 05 October 2014, 20:02:37 UTC |
| refs/tags/v0.9.19 | 3ad3a5a | Setting Release-Version v0.9.19 | 04 December 2014, 18:02:20 UTC |
| refs/tags/v0.9.20 | b040236 | Setting Release-Version v0.9.20 | 12 December 2014, 21:34:49 UTC |
| refs/tags/v0.9.21 | 1635a15 | Setting Release-Version v0.9.21 | 06 March 2015, 17:56:48 UTC |
| refs/tags/v0.9.9.1 | a994e78 | Setting Release-Version v9.9.1 | 02 July 2013, 08:32:27 UTC |
| refs/tags/v0.9.9.2 | 69f09a5 | Setting Release-Version v0.9.9.2 | 06 July 2013, 11:42:45 UTC |
| refs/tags/v1.0.0 | d527d78 | Setting Release-Version v1.0.0 | 14 November 2015, 15:39:28 UTC |
| refs/tags/v1.0.1 | efe685d | Merge branch 'nh13-nh_add_max_coverage' | 15 November 2015, 18:34:52 UTC |
| refs/tags/v1.0.2 | 0cb2697 | refactor to move data likelihood generation to a single function To prep the generation of GLs for non-calls. | 24 December 2015, 19:40:06 UTC |
| refs/tags/v1.1.0 | 39e5e4b | Merge pull request #328 from sambrightman/testspecifics Make some tests more specific | 03 November 2016, 11:25:39 UTC |
| refs/tags/v1.2.0 | 40155b4 | Merge pull request #453 from ekg/sensitive-defaults sensitive default filters | 09 April 2018, 15:09:32 UTC |
| refs/tags/v1.3.0 | 689d6d1 | Merge pull request #543 from ekg/coverage-limiting Skip high coverage regions by throwing away reads when they overlap a position with coverage above a given threshold | 29 May 2019, 10:56:46 UTC |
| refs/tags/v1.3.1 | 4cde5d3 | Merge pull request #545 from ekg/skip-coverage Skip coverage fixes | 03 June 2019, 13:29:43 UTC |
| refs/tags/v1.3.2 | 54bf409 | Merge pull request #571 from ekg/no-sort-alleles can we get away without sorting and removing "non-unique" alleles? | 06 October 2019, 08:14:31 UTC |
| refs/tags/v1.3.3 | ce156da | Release v1.3.3 | 13 December 2020, 13:19:12 UTC |
| refs/tags/v9.9.1 | a994e78 | Setting Release-Version v9.9.1 | 02 July 2013, 08:32:27 UTC |
| refs/tags/v9.9.11 | a97dbf8 | Setting Release-Version v9.9.11 | 16 January 2014, 23:29:42 UTC |
| refs/tags/v9.9.13 | 21a2951 | Setting Release-Version v9.9.13 | 14 February 2014, 21:39:33 UTC |
| refs/tags/v9.9.2 | be06174 | Setting Release-Version v9.9.2 | 04 July 2013, 16:41:50 UTC |
