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https://github.com/ekg/freebayes
19 January 2021, 09:51:49 UTC
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Revision Author Date Message Commit Date
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
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