| 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 |
| 8f0548e | Brad Langhorst | 02 May 2017, 21:47:47 UTC | Uses last instance of : instead of first to define sequence name Test suite passes | 02 May 2017, 21:50:27 UTC |
| 3b717e2 | Brad Langhorst | 02 May 2017, 18:09:42 UTC | add breaking test for contigs with colon in name | 02 May 2017, 21:50:16 UTC |
| 51b9862 | Jeremiah Wala | 25 April 2017, 16:55:37 UTC | merged conflicts with upstream Makefile for PR #338 | 25 April 2017, 16:55:37 UTC |
| b85e2a9 | rwhetten | 17 April 2017, 15:55:05 UTC | Update README.md Add information about freebayes-parallel script requirements | 17 April 2017, 15:55:05 UTC |
| 961e5f3 | Erik Garrison | 24 February 2017, 17:22:35 UTC | only compile Variant.o with c++11 | 24 February 2017, 17:22:35 UTC |
| b6d3d79 | Erik Garrison | 24 February 2017, 16:29:27 UTC | merge in new vcflib to resolve GCC version pinning problems | 24 February 2017, 16:29:40 UTC |
| 09d4ecf | walaj | 21 February 2017, 03:00:10 UTC | updated SeqLib to address issue #364 | 21 February 2017, 03:00:10 UTC |
| cb4b8a1 | walaj | 21 February 2017, 02:49:56 UTC | Merge branch 'master' of https://github.com/ekg/freebayes | 21 February 2017, 02:49:56 UTC |
| f15e66e | Erik Garrison | 06 February 2017, 22:43:29 UTC | bamleftalign: write the header, write BAM | 06 February 2017, 22:43:29 UTC |
| dc33860 | Jason Daniel Augustine Gilliland | 17 December 2016, 04:24:53 UTC | Note unstated dependency on zlib | 17 December 2016, 04:24:53 UTC |
| 253d992 | walaj | 15 December 2016, 04:02:18 UTC | updated build instructions in README | 15 December 2016, 04:02:18 UTC |
| b8d8e36 | walaj | 15 December 2016, 03:56:40 UTC | Fixed issue #346 regarding missing BAM header in bamleftalign | 15 December 2016, 03:56:40 UTC |
| 9e13293 | Sam Brightman | 23 November 2016, 06:29:50 UTC | Ensure make clean doesn't fail when bamtools is not built | 23 November 2016, 06:30:30 UTC |
| 61d2232 | Sam Brightman | 23 November 2016, 04:26:32 UTC | Enable VERBOSE_DEBUG logging for likelihoods * pulling logging macros out into a header * pass all parameters into probObservedAllelesGivenGenotype | 23 November 2016, 06:02:26 UTC |
| b6041c6 | Jeremiah Wala | 22 November 2016, 15:44:02 UTC | added CXX with CXXFLAGS patch to src/Makefile | 22 November 2016, 15:44:02 UTC |
| a9252fd | Jeremiah Wala | 21 November 2016, 21:52:32 UTC | separated CFLAGS and CXXFLAGS in src/Makefile | 21 November 2016, 21:52:32 UTC |
| 66e60e5 | Sam Brightman | 17 November 2016, 12:42:54 UTC | Fix typo in parameter parsing error message | 17 November 2016, 12:42:54 UTC |
| 83efe61 | Jeremiah Wala | 07 November 2016, 16:01:35 UTC | updated to latest SeqLib | 07 November 2016, 16:01:35 UTC |
| 2e05417 | Jeremiah Wala | 07 November 2016, 16:00:30 UTC | updated SeqLib, fixed CXXFLAGS passing, sep bamtools build | 07 November 2016, 16:00:30 UTC |
| 39e5e4b | Erik Garrison | 03 November 2016, 11:25:39 UTC | Merge pull request #328 from sambrightman/testspecifics Make some tests more specific | 03 November 2016, 11:25:39 UTC |
| 25d07ae | Erik Garrison | 03 November 2016, 11:24:07 UTC | Merge pull request #323 from mcshane/ad replace FORMAT/DPR annotation by FORMAT/AD | 03 November 2016, 11:24:07 UTC |
| af3c75f | Erik Garrison | 03 November 2016, 11:23:45 UTC | Merge pull request #324 from mcshane/AO-RO clarify header description of AO and RO | 03 November 2016, 11:23:45 UTC |
| fa641cc | Erik Garrison | 03 November 2016, 11:23:27 UTC | Merge pull request #327 from sambrightman/nh_fasta_iupac VCF's should not include IUPAC bases in the REF column. | 03 November 2016, 11:23:27 UTC |
| 3a5d168 | Sam Brightman | 11 October 2016, 15:02:18 UTC | Make some tests more specific | 11 October 2016, 15:02:18 UTC |
| 5aced98 | Sam Brightman | 01 October 2016, 13:52:24 UTC | Add tests for reference sequence characters | 11 October 2016, 13:56:16 UTC |
| 1f60c46 | Sam Brightman | 01 October 2016, 11:56:40 UTC | Refactor to avoid breaking detection of corrupt/compressed FASTAs | 11 October 2016, 13:56:16 UTC |
| 306e9bf | Sam Brightman | 01 October 2016, 10:35:06 UTC | Clean up whitespace and shorten code | 11 October 2016, 13:51:27 UTC |
| bdcc79e | Nils Homer | 10 June 2016, 01:25:43 UTC | VCF's should not include IUPAC bases in the REF column. | 11 October 2016, 13:51:27 UTC |
| 054b257 | Erik Garrison | 03 October 2016, 23:17:12 UTC | Merge pull request #316 from walaj/master SeqLib integration (HTSlib-based BamTools switch) | 03 October 2016, 23:17:12 UTC |
| 93fdbfe | Jeremiah Wala | 01 October 2016, 16:30:15 UTC | fixed numalignedbases issue in seqlib. fixed compile issue when VERBOSE_DEBUG on | 01 October 2016, 16:30:15 UTC |
| 39e7d24 | Jeremiah Wala | 01 October 2016, 14:07:52 UTC | updated seqlib | 01 October 2016, 14:07:52 UTC |
| a44df36 | Jeremiah Wala | 01 October 2016, 14:06:07 UTC | update seqlib | 01 October 2016, 14:06:07 UTC |
| 5675392 | Jeremiah Wala | 30 September 2016, 16:01:23 UTC | added back test suite | 30 September 2016, 16:01:23 UTC |
| 05f705a | Jeremiah Wala | 30 September 2016, 16:00:39 UTC | Merge branch 'master' of https://github.com/walaj/freebayes | 30 September 2016, 16:00:39 UTC |
| aa22eda | Jeremiah Wala | 30 September 2016, 16:00:28 UTC | added back region test suite | 30 September 2016, 16:00:28 UTC |
| 7c5735c | Jeremiah Wala | 30 September 2016, 15:47:33 UTC | updated seqlib | 30 September 2016, 15:47:33 UTC |
| 2bec394 | Jeremiah Wala | 30 September 2016, 14:36:47 UTC | update seqlib repos pointer | 30 September 2016, 14:36:47 UTC |
| 00c2adf | Jeremiah Wala | 30 September 2016, 14:23:44 UTC | Merge branch 'master' of https://github.com/walaj/freebayes | 30 September 2016, 14:23:44 UTC |
| 2c5b6fc | Jeremiah Wala | 30 September 2016, 14:23:38 UTC | removed debug print statement | 30 September 2016, 14:23:38 UTC |
| a369be9 | Jeremiah Wala | 30 September 2016, 13:47:06 UTC | removed initial print statement | 30 September 2016, 13:47:06 UTC |
| 375552f | Shane McCarthy | 30 September 2016, 13:31:00 UTC | clarify header description of AO and RO Closes #142 | 30 September 2016, 13:35:49 UTC |
| 145d00d | Shane McCarthy | 30 September 2016, 13:01:09 UTC | replace FORMAT/DPR annotation by FORMAT/AD DPR is mislabeled as a `Number=A` field, but writing out `Number=R` values. Also, as @nh13 noticed, the REF allele count was wrong anyway - printing the total depth rather than the REF depth. Replace by FORMAT/AD which is a Number=R field now defined in the spec. Also need to bump the VCF version to 4.2 (`Number=R` was introduced in 4.2, but AD in 4.3) Fixes #267 | 30 September 2016, 13:14:02 UTC |
| 4ce45ec | Jeremiah Wala | 29 September 2016, 23:16:40 UTC | merged with upstream | 29 September 2016, 23:16:40 UTC |
| d57be62 | Erik Garrison | 29 September 2016, 18:14:02 UTC | Merge pull request #319 from sambrightman/uniquesampleids Ensure FreeBayes fails on multiple BAMs with conflicting read groups | 29 September 2016, 18:14:02 UTC |
| a5f71a9 | Erik Garrison | 29 September 2016, 18:13:47 UTC | Merge pull request #318 from sambrightman/regiontests Fix region tests and ensure that they are used | 29 September 2016, 18:13:47 UTC |
| fc96d2f | Jeremiah Wala | 29 September 2016, 15:15:04 UTC | lighter seqlib | 29 September 2016, 15:15:04 UTC |
| 8b628d1 | Jeremiah Wala | 15 September 2016, 18:42:02 UTC | better seqlib integration for bamleftalign | 15 September 2016, 18:42:02 UTC |
| 53f594b | Sam Brightman | 15 September 2016, 10:37:02 UTC | Add similar check for different sequencing technologies Unsure if stricly necessary, but seems like an error to map the same read group ID to different PL. Previously the map entry was blindly over-written. Add tests for this. | 15 September 2016, 14:35:27 UTC |
| ee1ba6a | Sam Brightman | 15 September 2016, 12:43:04 UTC | Ensure failure when read group to sample mapping is not clear * Check BAM headers individually so that bamtools does not make them unique before FreeBayes can check them. * Add basic tests for multiple BAM input. This does not work for standard input, because the stream would be used up on the first read. It seems less likely that standard input is used in combination with other BAMs (but possible). More sustainable would be adding a method to MultiBamReader to provide the raw header text. | 15 September 2016, 14:35:27 UTC |
| 8d0068e | Sam Brightman | 14 September 2016, 10:07:06 UTC | Fix region tests and ensure that they are used * Region tests were not actually being run by 'make test' * Region tests were failing * Fix variant detection at start of region (caused by commit 840b412) * Add tests for IGV-style regions (commit a412676) * Refactor tests are little * Add -S for old samtools This is an *attempted* fix for the first-of-target problem; I cannot be sure that it is a correct fix. There is another line that increments the counter just above, but from what I can tell this one should stay as it is. | 14 September 2016, 17:19:44 UTC |
| 9e8f5a5 | Jeremiah Wala | 05 September 2016, 20:09:19 UTC | tested multi-bam run | 05 September 2016, 20:09:19 UTC |
| 2fbc006 | Jeremiah Wala | 05 September 2016, 19:22:47 UTC | simplified BamTools / SeqLib switch syntax with macros | 05 September 2016, 19:22:47 UTC |
| 40ea253 | Jeremiah Wala | 05 September 2016, 17:36:42 UTC | makefile typo | 05 September 2016, 17:36:42 UTC |
| 9873140 | Jeremiah Wala | 05 September 2016, 16:33:55 UTC | move to seqlib | 05 September 2016, 16:33:55 UTC |
| 062a669 | Jeremiah Wala | 22 August 2016, 20:12:57 UTC | added seqlib | 22 August 2016, 20:12:57 UTC |
| dbb6160 | Erik Garrison | 23 June 2016, 17:20:50 UTC | Merge pull request #299 from zeeev/master fixing min_depth | 23 June 2016, 17:20:50 UTC |
