| 9965815 | Erik Garrison | 05 October 2019, 21:38:02 UTC | can we get away without sorting and removing "non-unique" alleles? | 05 October 2019, 21:38:02 UTC |
| aa2ace8 | Erik Garrison | 10 July 2019, 12:48:23 UTC | update readme to reflect new tools | 10 July 2019, 12:48:23 UTC |
| 85d7bfc | Erik Garrison | 18 June 2019, 15:20:20 UTC | further improve documentation | 18 June 2019, 15:20:20 UTC |
| c2d15ea | Erik Garrison | 18 June 2019, 14:44:55 UTC | Merge branch 'master' of github.com:ekg/freebayes | 18 June 2019, 14:44:55 UTC |
| 2d7fc0f | Erik Garrison | 18 June 2019, 14:44:42 UTC | simplify documenation further | 18 June 2019, 14:44:42 UTC |
| 8fb17e8 | Erik Garrison | 18 June 2019, 14:41:39 UTC | reorder the help text | 18 June 2019, 14:41:39 UTC |
| 06fe585 | Erik Garrison | 04 June 2019, 13:21:34 UTC | Merge pull request #512 from wlokhorst/Python3_compatible Python3 compatible | 04 June 2019, 13:21:34 UTC |
| b4dd478 | Erik Garrison | 04 June 2019, 11:57:43 UTC | Merge pull request #546 from ekg/force-0-qual force quality to be 0 when no quality string given | 04 June 2019, 11:57:43 UTC |
| 9bfee20 | Erik Garrison | 04 June 2019, 10:13:41 UTC | force quality to be 0 when no quality string given In response to #509. | 04 June 2019, 10:13:41 UTC |
| 5eb71a3 | Erik Garrison | 04 June 2019, 08:30:13 UTC | correct my email | 04 June 2019, 08:30:13 UTC |
| 4cde5d3 | Erik Garrison | 03 June 2019, 13:29:43 UTC | Merge pull request #545 from ekg/skip-coverage Skip coverage fixes | 03 June 2019, 13:29:43 UTC |
| ffcee0d | Erik Garrison | 03 June 2019, 13:16:34 UTC | 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 |
| 4b8845a | Erik Garrison | 03 June 2019, 07:59:51 UTC | change test to match current (correct!) behavior | 03 June 2019, 07:59:51 UTC |
| e666b5b | Erik Garrison | 02 June 2019, 15:02:35 UTC | correct mistake with registered alignment skip coverage exclusion | 02 June 2019, 15:02:35 UTC |
| 61d63a9 | Erik Garrison | 02 June 2019, 14:23:25 UTC | greatly reduce RegisteredAlignment's size by removing Parameters object This never should have been included in this structure, as it would have massively increased the size of the RegisteredAlignment. This might have been the cause of memory problems people have encountered! | 02 June 2019, 14:23:25 UTC |
| 7e863ee | Erik Garrison | 30 May 2019, 21:30:40 UTC | Merge pull request #544 from ekg/skip-depth-partials avoid position skipping logic when getting partial alignments covering haplotype calls | 30 May 2019, 21:30:40 UTC |
| fbaed2e | Erik Garrison | 30 May 2019, 16:01:51 UTC | 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 |
| e09b591 | Erik Garrison | 30 May 2019, 08:37:56 UTC | remove gitter badge | 30 May 2019, 08:37:56 UTC |
| af7bbea | Erik Garrison | 30 May 2019, 08:37:16 UTC | set the correct image file | 30 May 2019, 08:37:16 UTC |
| da9e8fe | Erik Garrison | 30 May 2019, 08:25:32 UTC | correct skip-coverage parameter name in parameters.cpp | 30 May 2019, 08:25:32 UTC |
| 689d6d1 | Erik Garrison | 29 May 2019, 10:56:46 UTC | 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 |
| 9a32a36 | Erik Garrison | 29 May 2019, 10:42:56 UTC | minor code cleanup for clarity | 29 May 2019, 10:42:56 UTC |
| 37b03fe | Erik Garrison | 29 May 2019, 10:40:55 UTC | document changes to coverage limiting and provide an example | 29 May 2019, 10:40:55 UTC |
| 69ed30f | Erik Garrison | 29 May 2019, 10:34:46 UTC | correct number of tests | 29 May 2019, 10:34:46 UTC |
| 43d35df | Erik Garrison | 29 May 2019, 10:23:07 UTC | Merge branch 'master' of github.com:ekg/freebayes into coverage-limiting | 29 May 2019, 10:23:07 UTC |
| 2d02324 | Erik Garrison | 29 May 2019, 10:19:30 UTC | to avoid future confusion, change terminology of coverage capping and limiting rather than max-coverage | 29 May 2019, 10:19:30 UTC |
| e9342aa | Erik Garrison | 29 May 2019, 10:09:36 UTC | correct documentation of --cap-coverage | 29 May 2019, 10:09:36 UTC |
| 2ef1ea4 | Erik Garrison | 29 May 2019, 10:05:14 UTC | correct capping conditional and implement test | 29 May 2019, 10:05:14 UTC |
| 4269f7c | Erik Garrison | 29 May 2019, 09:52:27 UTC | implement pre-read parsing coverage capping mechanism | 29 May 2019, 09:52:27 UTC |
| 3c81125 | Erik Garrison | 28 May 2019, 17:00:18 UTC | cap coverage and throw away our observations when the tail position in the read exceeds a given threshold | 28 May 2019, 17:00:18 UTC |
| ef09fe2 | Erik Garrison | 28 May 2019, 15:48:23 UTC | make static builds work properly | 28 May 2019, 15:48:23 UTC |
| a78ffc0 | Erik Garrison | 06 May 2019, 13:07:37 UTC | Merge pull request #535 from Nheyer/master fix for Gvcf Depth, and added format flags | 06 May 2019, 13:07:37 UTC |
| 44bd4cb | Nick Heyer | 03 May 2019, 17:44:35 UTC | I can type... | 03 May 2019, 17:44:35 UTC |
| 61acc4a | Nheyer | 02 May 2019, 17:29:18 UTC | syntax | 02 May 2019, 17:29:18 UTC |
| a39615e | Nheyer | 02 May 2019, 17:24:01 UTC | fix minDepth logic | 02 May 2019, 17:24:01 UTC |
| cc77002 | Nheyer | 02 May 2019, 17:19:14 UTC | Because apparently I cant capitalize things... | 02 May 2019, 17:19:14 UTC |
| 25d73bf | Nheyer | 02 May 2019, 17:08:47 UTC | optimized minDepth logic, and added format fields | 02 May 2019, 17:08:47 UTC |
| 0f430f2 | Nick Heyer | 29 April 2019, 17:39:23 UTC | Fix gvcf Depth | 29 April 2019, 17:39:23 UTC |
| 8a0dbee | Erik Garrison | 22 April 2019, 08:20:29 UTC | Merge pull request #532 from Nheyer/master Fix for gvcf chunk size, as well as an addition of the ability to use minimal gvcf chunking | 22 April 2019, 08:20:29 UTC |
| fbbba13 | Nick Heyer | 21 April 2019, 21:54:30 UTC | small fixed, and adding tests | 21 April 2019, 21:54:30 UTC |
| a4fc253 | Nick Heyer | 19 April 2019, 16:18:19 UTC | Spelling | 19 April 2019, 16:18:19 UTC |
| ec7ddb5 | Nick Heyer | 19 April 2019, 13:42:58 UTC | fix for gvcf size being over, as well as adding a flag to allow for gvcf chunks of size 1 | 19 April 2019, 13:42:58 UTC |
| 2496097 | Nick Heyer | 19 April 2019, 13:37:55 UTC | Merge branch 'master' of github.com:Nheyer/freebayes This is the branch I am using to create pull requests for the main freebases distrobution | 19 April 2019, 13:37:55 UTC |
| 3827b18 | Nick Heyer | 18 April 2019, 21:53:13 UTC | testing | 18 April 2019, 21:53:13 UTC |
| d15209e | Erik Garrison | 14 February 2019, 14:26:48 UTC | Merge pull request #518 from ekg/cnv-map-help clarify how to use the CNV map | 14 February 2019, 14:26:48 UTC |
| fed2400 | Erik Garrison | 14 February 2019, 14:13:45 UTC | clarify how to use the CNV map | 14 February 2019, 14:13:45 UTC |
| 4a2b38d | wlokhorst | 03 January 2019, 15:21:18 UTC | Update hwe.py | 03 January 2019, 15:21:18 UTC |
| 99be5ad | wlokhorst | 03 January 2019, 15:20:13 UTC | Update dirichlet.py | 03 January 2019, 15:20:13 UTC |
| 651d809 | wlokhorst | 03 January 2019, 15:17:43 UTC | Update allelebayes.py | 03 January 2019, 15:17:43 UTC |
| 3fa35d3 | wlokhorst | 03 January 2019, 15:05:06 UTC | Update allelebayes.py | 03 January 2019, 15:05:06 UTC |
| da95a71 | wlokhorst | 03 January 2019, 15:02:24 UTC | Update dirichlet.py | 03 January 2019, 15:02:24 UTC |
| 24277d1 | wlokhorst | 03 January 2019, 15:01:16 UTC | Update hwe.py | 03 January 2019, 15:01:16 UTC |
| 3c4e775 | wlokhorst | 03 January 2019, 14:58:01 UTC | Update coverage_to_regions.py | 03 January 2019, 14:58:01 UTC |
| 1be415c | wlokhorst | 03 January 2019, 14:47:39 UTC | Update fasta_generate_regions.py | 03 January 2019, 14:47:39 UTC |
| 29c4002 | Erik Garrison | 25 August 2018, 10:05:59 UTC | Merge pull request #487 from ekg/document-params clarify the effect of allele exclusion filters and document best practices | 25 August 2018, 10:05:59 UTC |
| 133bbb7 | Erik Garrison | 24 August 2018, 07:52:05 UTC | 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 |
| 40155b4 | Erik Garrison | 09 April 2018, 15:09:32 UTC | Merge pull request #453 from ekg/sensitive-defaults sensitive default filters | 09 April 2018, 15:09:32 UTC |
| 6725791 | Erik Garrison | 30 March 2018, 09:10:17 UTC | match tests to current default settings | 30 March 2018, 09:10:17 UTC |
| 7c3d4a4 | Erik Garrison | 28 March 2018, 17:08:58 UTC | set --min-repeat-entropy 1 and --min-alternate-fraction 0.05 These have been my favored parameters for some time. Users may need to adjust downstream filtering to account for changes in allele reporting. I will cut a new version after vetting this with other users. | 28 March 2018, 17:08:58 UTC |
| c15b070 | Erik Garrison | 14 February 2018, 14:26:47 UTC | Merge pull request #448 from ekg/compound-haplotype resolve #437 | 14 February 2018, 14:26:47 UTC |
| 03e9156 | Erik Garrison | 14 February 2018, 12:41:00 UTC | Merge pull request #439 from williamrowell/master replace --haplotype-window with --haplotype-length | 14 February 2018, 12:41:00 UTC |
| 632eb29 | Erik Garrison | 14 February 2018, 11:07:31 UTC | resolve #437 | 14 February 2018, 11:07:31 UTC |
| a180635 | Erik Garrison | 01 February 2018, 12:57:52 UTC | Merge pull request #443 from ekg/call-on-ref-N allow calling on N-matching reference bases | 01 February 2018, 12:57:52 UTC |
| b5ccca1 | Erik Garrison | 01 February 2018, 12:25:19 UTC | allow calling on N-matching bases | 01 February 2018, 12:25:19 UTC |
| b01663e | William Rowell | 22 January 2018, 21:24:34 UTC | replace --haplotype-window with --haplotype-length replaced occurrences of --haplotype-window in examples with --haplotype-length, as described in https://groups.google.com/d/msg/freebayes/FBOgspri3QE/Fw5fQ2CuFQUJ | 22 January 2018, 21:24:34 UTC |
| 49413aa | Erik Garrison | 07 November 2017, 20:21:57 UTC | Merge pull request #431 from ekg/building remove gdb flag from compilation | 07 November 2017, 20:21:57 UTC |
| 6a2fbdb | Erik Garrison | 07 November 2017, 19:58:09 UTC | remove gdb flag from compilation | 07 November 2017, 19:58:09 UTC |
| 225a3d6 | Erik Garrison | 07 November 2017, 18:03:24 UTC | Merge pull request #429 from Biomatters/master Support for compilation with Cygwin 64 | 07 November 2017, 18:03:24 UTC |
| ba4b26c | rainbowgoblin | 06 November 2017, 01:35:03 UTC | Support for compilation with Cygwin 64 | 06 November 2017, 01:35:03 UTC |
| 61527c5 | Erik Garrison | 13 October 2017, 09:23:20 UTC | Merge pull request #426 from ekg/error-reporting Give warning when there is a likely mismatch between alignment and reference sequence | 13 October 2017, 09:23:20 UTC |
| f5dd0b5 | Erik Garrison | 12 October 2017, 21:35:05 UTC | Merge pull request #340 from sambrightman/likelihood-debug-logging Enable VERBOSE_DEBUG logging for likelihoods | 12 October 2017, 21:35:05 UTC |
| 3346c60 | Erik Garrison | 12 October 2017, 21:31:06 UTC | clarify that alignments mapping past the end of contigs indicates a potential problem with the input | 12 October 2017, 21:31:06 UTC |
| 8d2b3a0 | Erik Garrison | 23 August 2017, 15:05:16 UTC | Merge pull request #417 from ekg/bugfix resolve #406 | 23 August 2017, 15:05:16 UTC |
| df9bb28 | Erik Garrison | 23 August 2017, 00:43:35 UTC | 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 |
| d784cf8 | Erik Garrison | 13 July 2017, 09:11:57 UTC | Merge pull request #404 from ekg/build Fixes the build by correcting compile flags | 13 July 2017, 09:11:57 UTC |
| b185873 | Erik Garrison | 13 July 2017, 08:50:37 UTC | list bamleftalign before objects in build | 13 July 2017, 08:50:37 UTC |
| 1f3b002 | Erik Garrison | 12 July 2017, 23:04:00 UTC | Merge branch 'build' of github.com:ekg/freebayes | 12 July 2017, 23:04:00 UTC |
| f26dc98 | Erik Garrison | 12 July 2017, 23:01:38 UTC | hack out duplicate htslib from build | 12 July 2017, 23:01:38 UTC |
| f3a4441 | Erik Garrison | 12 July 2017, 21:25:41 UTC | updates vcflib/tabixpp/htslib | 12 July 2017, 21:25:41 UTC |
| 22bf987 | Erik Garrison | 12 July 2017, 21:20:54 UTC | sync with newer htslib So at least we have the same one in vcflib and seqlib. Not ideal. | 12 July 2017, 21:20:54 UTC |
| 948781b | Erik Garrison | 12 July 2017, 18:12:55 UTC | build two htslibs... This isn't ideal but it seems to be required given the vcflib/SeqLib divide. | 12 July 2017, 18:12:55 UTC |
| 1560765 | Erik Garrison | 12 July 2017, 17:47:18 UTC | include htslib statically | 12 July 2017, 17:47:18 UTC |
| 9da78c4 | Erik Garrison | 12 July 2017, 17:24:59 UTC | add htslib to library search path (resolves #405) | 12 July 2017, 17:24:59 UTC |
| 8e630c4 | Erik Garrison | 12 July 2017, 16:02:40 UTC | fix build for bamleftalign as well | 12 July 2017, 16:02:40 UTC |
| b6fe145 | Erik Garrison | 12 July 2017, 15:59:41 UTC | resolve build problems We shouldn't treating the .a static libs as objects. | 12 July 2017, 15:59:41 UTC |
| b067b6e | Erik Garrison | 12 July 2017, 14:36:33 UTC | Merge branch 'walaj-master' | 12 July 2017, 14:36:33 UTC |
| 7dc5be8 | Erik Garrison | 12 July 2017, 14:34:48 UTC | Merge branch 'master' of https://github.com/walaj/freebayes into walaj-master | 12 July 2017, 14:34:48 UTC |
| f439104 | Erik Garrison | 09 July 2017, 13:11:40 UTC | Merge pull request #403 from ekg/ploidy Set global per-sample ploidy via the CNV map | 09 July 2017, 13:11:40 UTC |
| 89d2312 | Erik Garrison | 09 July 2017, 12:55:44 UTC | *actually* use SAM rather than BAM to avoid samtools version weirdness | 09 July 2017, 12:55:44 UTC |
| 4d5c3c1 | Erik Garrison | 09 July 2017, 11:02:12 UTC | avoid dependency on samtools version in test | 09 July 2017, 11:02:12 UTC |
| 241e3fc | Erik Garrison | 09 July 2017, 10:19:14 UTC | Merge branch 'master' of github.com:ekg/freebayes | 09 July 2017, 10:19:14 UTC |
| b5b5432 | Erik Garrison | 09 July 2017, 10:18:51 UTC | allow setting of per-sample global ploidy via the --cnv-map | 09 July 2017, 10:18:51 UTC |
| 208d9c0 | Erik Garrison | 09 July 2017, 10:18:20 UTC | Merge pull request #402 from ekg/haplotypes Improve handling of complex alleles | 09 July 2017, 10:18:20 UTC |
| 00afac8 | Erik Garrison | 09 July 2017, 09:30:19 UTC | Merge pull request #336 from sambrightman/master Fix typo in parameter parsing error message | 09 July 2017, 09:30:19 UTC |
| 8840f10 | Erik Garrison | 09 July 2017, 09:29:58 UTC | Merge pull request #341 from sambrightman/make-clean Ensure make clean doesn't fail when bamtools is not built | 09 July 2017, 09:29:58 UTC |
| 4cef622 | Erik Garrison | 09 July 2017, 09:29:25 UTC | Merge pull request #352 from jdagilliland/docfix Note unstated dependency on zlib | 09 July 2017, 09:29:25 UTC |
| 2ea5a89 | Erik Garrison | 09 July 2017, 09:29:15 UTC | Merge pull request #378 from rwhetten/patch-1 Update README.md | 09 July 2017, 09:29:15 UTC |
| f1e6993 | Erik Garrison | 09 July 2017, 09:28:52 UTC | remove temporary files after test | 09 July 2017, 09:28:52 UTC |
| 880cf1a | Erik Garrison | 09 July 2017, 09:21:13 UTC | complete rewrite of haplotype allele processing freebayes was no longer natively detecting certain types of complex alleles. To resolve this I refactored the allele clumping algorithm. Some tests required alteration due to changes in the allele quality assignment. Alleles need to have assigned quality to be considered. | 09 July 2017, 09:21:13 UTC |
| f069ec6 | Erik Garrison | 28 June 2017, 08:51:36 UTC | Merge pull request #383 from bwlang/grch38_hla_support Grch38 hla support | 28 June 2017, 08:51:36 UTC |
