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 |
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 |
f15e66e | Erik Garrison | 06 February 2017, 22:43:29 UTC | bamleftalign: write the header, write BAM | 06 February 2017, 22:43:29 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 |
3fcd51e | Erik Garrison | 23 June 2016, 17:20:42 UTC | Merge pull request #290 from nh13/nh_fixup_max_coverage_merge Bug fix in merge 96e85182c4cd1c462cf49ca06b858da8c7b99c44. | 23 June 2016, 17:20:42 UTC |
4d700a9 | zev kronenberg | 20 June 2016, 18:59:39 UTC | fixing min depth | 20 June 2016, 18:59:39 UTC |
9b57a01 | Nils Homer | 05 June 2016, 02:32:52 UTC | Bug fix in merge 96e85182c4cd1c462cf49ca06b858da8c7b99c44. We should not skip when we have *enough* coverage, rather we do not need to downsample when we have *enough* coverage. | 05 June 2016, 02:32:52 UTC |
41c1313 | Erik Garrison | 01 June 2016, 17:42:46 UTC | Merge pull request #280 from zeeev/master Updating VCFLIB submodule and format change | 01 June 2016, 17:42:46 UTC |
cec5717 | zev kronenberg | 22 May 2016, 23:18:13 UTC | munged the path, correct now | 22 May 2016, 23:18:13 UTC |
03df9ef | zev kronenberg | 22 May 2016, 23:07:54 UTC | new paths | 22 May 2016, 23:07:54 UTC |
beee73d | zev kronenberg | 22 May 2016, 22:59:21 UTC | mod test make | 22 May 2016, 22:59:21 UTC |
9e4fd0f | zev kronenberg | 22 May 2016, 22:44:46 UTC | added vcflib | 22 May 2016, 22:44:46 UTC |
b39dd20 | zev kronenberg | 22 May 2016, 22:42:33 UTC | removing vcflib | 22 May 2016, 22:42:33 UTC |
95a9231 | zev kronenberg | 22 May 2016, 22:36:05 UTC | removing old vcflib | 22 May 2016, 22:36:05 UTC |
262d614 | zev kronenberg | 22 May 2016, 22:10:07 UTC | vcf -> vcflib | 22 May 2016, 22:10:07 UTC |
112e6b6 | zev kronenberg | 22 May 2016, 22:07:46 UTC | ekg -> vcflib | 22 May 2016, 22:07:46 UTC |
86022a1 | zev kronenberg | 22 May 2016, 21:45:16 UTC | added phtreads | 22 May 2016, 21:45:16 UTC |
130da83 | zev kronenberg | 22 May 2016, 18:21:33 UTC | htslib now in | 22 May 2016, 18:21:33 UTC |
932495a | zev kronenberg | 21 May 2016, 20:08:16 UTC | updating the pointer | 21 May 2016, 20:08:16 UTC |
280a099 | zev kronenberg | 21 May 2016, 19:58:26 UTC | MIN -> MIN_DP | 21 May 2016, 19:58:26 UTC |
d466dde | Erik Garrison | 19 April 2016, 16:00:30 UTC | remove reference to old version of freebayes from README | 19 April 2016, 16:00:30 UTC |
357f175 | Erik Garrison | 29 March 2016, 12:26:56 UTC | add bgziptabix script to bgzip and tabix with one command For easier scripting, that's all. For example: freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam | bgziptabix x.vcf.gz | 29 March 2016, 12:26:56 UTC |
9e98366 | Erik Garrison | 19 March 2016, 14:47:54 UTC | Merge pull request #156 from tseemann/script_headers Replace hash-bang lines with /usr/bin/env for compatibility | 19 March 2016, 14:47:54 UTC |
bc5a6b4 | Erik Garrison | 19 March 2016, 14:47:38 UTC | Merge pull request #259 from mcshane/feature/gvcf_ref_allele set REF allele for gVCF records from startPos | 19 March 2016, 14:47:38 UTC |
adde0f9 | Erik Garrison | 19 March 2016, 14:47:27 UTC | Merge pull request #252 from huddlej/master Add support for reading SAM 1.3 CIGAR operations in bamleftalign | 19 March 2016, 14:47:27 UTC |
0045411 | Erik Garrison | 19 March 2016, 14:47:16 UTC | Merge pull request #248 from holtgrewe/feature/contig_header_lines Writing out ##contig=<> lines in VCF header | 19 March 2016, 14:47:16 UTC |
94d1669 | Shane McCarthy | 10 March 2016, 20:52:36 UTC | set REF allele for gVCF records from startPos Fixes #258 | 10 March 2016, 20:52:36 UTC |
bbaddd8 | John Huddleston | 24 February 2016, 17:27:50 UTC | Add support for reading SAM 1.3 CIGAR operations in bamleftalign. | 24 February 2016, 17:27:50 UTC |
3ce827d | Erik Garrison | 17 February 2016, 12:08:59 UTC | Merge pull request #247 from holtgrewe/feature/add_format_dpr Writing out FORMAT/DPR tag in addition to FORMAT/DP and FORMAT/AO | 17 February 2016, 12:08:59 UTC |
bfa9f57 | Erik Garrison | 17 February 2016, 12:02:09 UTC | Merge pull request #246 from holtgrewe/feature/comma_in_region Ignoring commas in region specification | 17 February 2016, 12:02:09 UTC |
c2f6865 | Manuel Holtgrewe | 17 February 2016, 08:39:19 UTC | Writing out ##contig=<> lines in VCF header | 17 February 2016, 08:40:13 UTC |
3ed4094 | Manuel Holtgrewe | 17 February 2016, 08:27:15 UTC | Writing out FORMAT/DPR tag in addition to FORMAT/DP and FORMAT/AO This makes the output more similar to bcftools call. | 17 February 2016, 08:27:48 UTC |
a412676 | Manuel Holtgrewe | 17 February 2016, 08:12:25 UTC | Ignoring commas in region specification This allows specifying regions such as 1:68,152,354-68,152,418 for the --region parameter which makes copy and paste with UCSC and IGV genome browsers easier. | 17 February 2016, 08:12:25 UTC |
7ceb532 | Erik Garrison | 17 February 2016, 05:43:41 UTC | Merge pull request #245 from holtgrewe/feature/strict_vcf_flag Adding --strict-vcf flag | 17 February 2016, 05:43:41 UTC |
5815624 | Manuel Holtgrewe | 16 February 2016, 12:09:46 UTC | Adding --strict-vcf flag | 16 February 2016, 12:09:46 UTC |
0cb2697 | Erik Garrison | 24 December 2015, 19:40:06 UTC | 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 |
683b3cc | Erik Garrison | 07 December 2015, 02:35:10 UTC | resolves #225 I was recording nonCalls even when we weren't in gVCF mode. As a result, they would build up causing huge memory usage. I haven't tested this at scale but the issue is pretty clear internally--- programmer error. | 07 December 2015, 02:35:10 UTC |
efe685d | Erik Garrison | 15 November 2015, 18:34:52 UTC | Merge branch 'nh13-nh_add_max_coverage' | 15 November 2015, 18:34:52 UTC |
96e8518 | Erik Garrison | 15 November 2015, 18:34:05 UTC | Merge branch 'nh_add_max_coverage' of https://github.com/nh13/freebayes into nh13-nh_add_max_coverage Also add info about the new option to parameters. Conflicts: src/Parameters.cpp src/freebayes.cpp | 15 November 2015, 18:34:05 UTC |
34cac0a | Erik Garrison | 15 November 2015, 18:16:01 UTC | Merge pull request #216 from ekg/gvcf-chunk gVCF chunk | 15 November 2015, 18:16:01 UTC |
728cac1 | Erik Garrison | 15 November 2015, 18:14:17 UTC | Merge pull request #153 from ryan-williams/patch-1 fix some README typos | 15 November 2015, 18:14:17 UTC |
f93173d | Erik Garrison | 15 November 2015, 18:05:12 UTC | Merge pull request #211 from travc/unique-bam-file-check duplicate bam file check | 15 November 2015, 18:05:12 UTC |
c5f0472 | Erik Garrison | 15 November 2015, 18:04:49 UTC | Merge pull request #209 from travc/master bit stricter BED processing | 15 November 2015, 18:04:49 UTC |
8916bd0 | Erik Garrison | 15 November 2015, 18:02:01 UTC | add test for gVCF chunking | 15 November 2015, 18:02:01 UTC |
99d5ce1 | Erik Garrison | 15 November 2015, 18:00:29 UTC | Merge branch 'master' of github.com:ekg/freebayes Conflicts: src/ResultData.cpp | 15 November 2015, 18:00:29 UTC |
a765afb | Erik Garrison | 15 November 2015, 17:57:01 UTC | Merge pull request #215 from dnanexus-rnd/mlin-gvcf-segfault gvcf bugfixes | 15 November 2015, 17:57:01 UTC |
551bb67 | Erik Garrison | 15 November 2015, 17:55:55 UTC | adds gvcf chunking Untested in this commit. I need to merge @mlin's changes. | 15 November 2015, 17:55:55 UTC |
6d7d7ab | Mike Lin | 14 November 2015, 21:47:26 UTC | Bugfix: prevent divide-by-zero in ResultData::gvcf arising from off-by-one position | 14 November 2015, 21:49:36 UTC |
26255fa | Mike Lin | 14 November 2015, 21:33:33 UTC | Bugfix: prevent segfault from calling ResultData::gvcf with empty input | 14 November 2015, 21:49:36 UTC |
d527d78 | Erik Garrison | 14 November 2015, 15:39:28 UTC | Setting Release-Version v1.0.0 | 14 November 2015, 15:39:28 UTC |
d37dc27 | Erik Garrison | 14 November 2015, 15:26:08 UTC | Merge pull request #213 from ekg/gvcf-support add gVCF support | 14 November 2015, 15:26:08 UTC |
a2176b7 | Erik Garrison | 14 November 2015, 15:16:32 UTC | 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 |
2f938b0 | Travis Collier | 14 November 2015, 08:36:37 UTC | fixed test to have tab-deliminated BED | 14 November 2015, 08:36:37 UTC |
d0ce5be | Travis Collier | 14 November 2015, 08:25:12 UTC | undo slightly more strict BED reader | 14 November 2015, 08:25:12 UTC |
c43856b | Travis Collier | 14 November 2015, 08:24:07 UTC | undo slightly more strict BED reader | 14 November 2015, 08:24:07 UTC |
e1479a1 | Travis Collier | 14 November 2015, 08:16:51 UTC | Check for duplicate bam files | 14 November 2015, 08:16:51 UTC |
4d99c14 | Travis Collier | 13 November 2015, 23:32:44 UTC | Skip lines with too few '\t' delim fields to handle track, browser, ect header lines | 13 November 2015, 23:32:44 UTC |
ecdc994 | Erik Garrison | 13 November 2015, 17:55:09 UTC | resolve #205 and add test for spliced read handling | 13 November 2015, 17:55:09 UTC |
ab0bcf3 | Erik Garrison | 11 November 2015, 21:49:00 UTC | Merge pull request #186 from mckinsel/fix_bash_sp Fix freebayes-parallel word splitting | 11 November 2015, 21:49:00 UTC |
7b78a8c | Marcus Kinsella | 05 August 2015, 19:14:23 UTC | Prevent word splitting in freebayes-parallel args You might want to call freebayes-parallel with filenames with spaces in them: freebayes-parallel 'a regions file.txt' 2 -f 'some reads.fasta' alns.bam But, when the argument array is assigned to the command string, everything gets split on spaces, and freebayes would do something like complain about not being able to find a file called "some". This change keeps the arguments in an array and prevents splitting of the regionsfile. Two tests are included with filenames that have spaces in them. | 11 November 2015, 21:11:56 UTC |
bfd9832 | Erik Garrison | 23 October 2015, 15:06:31 UTC | resolves #206 | 23 October 2015, 15:06:31 UTC |
cd648aa | Erik Garrison | 16 October 2015, 20:42:51 UTC | bail out if freebayes is given a corrupted or compressed reference | 16 October 2015, 20:42:51 UTC |