c0bf07cb78
Merge pull request #1559 from broadinstitute/rhl_htsjdk_2.9.1_picard_2.9.0
...
Move htsjdk to ver 2.9.1 and picard to ver 2.9.0
2017-02-23 14:32:44 -05:00
91339c12c9
Move htsjdk to ver 2.9.1 and picard to ver 2.9.0
2017-02-22 19:01:26 -05:00
5c178c2a84
Merge pull request #1553 from broadinstitute/rhl_latv_split_nocall_1518
...
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
2017-02-22 18:54:26 -05:00
61875e4dfa
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
2017-02-22 17:57:59 -05:00
b9a43cc35e
Merge pull request #1557 from broadinstitute/rhl_ggvcfs_input_prior_1532
...
Total ploidy does not have to equal to the number of priors
2017-02-20 22:21:25 -05:00
3c347c1385
Total ploidy does not have to equal to the number of priors
2017-02-20 20:28:41 -05:00
c55c77ab27
Merge pull request #1555 from broadinstitute/rhl_htsjdk_2.9.0_picard_2.8.3
...
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
2017-02-17 13:54:17 -05:00
ab75b08ea7
Remove unused compressed_block_size and close BlockCompressedInputStream
2017-02-17 12:22:53 -05:00
1d36d9fd69
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
2017-02-17 07:03:03 -05:00
67baa9046c
Merge pull request #1550 from broadinstitute/rhl_fix_splitncigarreads_doc_1549
...
Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc
2017-01-18 17:06:06 -05:00
dce2e29ade
Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc
2017-01-18 15:11:52 -05:00
7c0e51396f
Merge pull request #1539 from broadinstitute/rhl_hc_disable_badmatefilter_1443
...
Allow disabling of BadMateFilter in HaplotypeCaller
2017-01-18 12:39:22 -05:00
bfa633a90f
Merge pull request #1548 from broadinstitute/rhl_synchonize_upstream_del_1188
...
Make upstreamDeletionsLoc Thread Safe
2017-01-13 14:57:05 -05:00
1f6645539a
Make upstreamDeletionsLoc ThreadLocal
2017-01-12 14:09:24 -05:00
f092e1438d
Allow disabling of BadMateFilter in HaplotypeCaller
2017-01-11 14:49:45 -05:00
bb87730ddc
Merge pull request #1546 from broadinstitute/rhl_annot_warn_1540
...
Log annotation warning once if using multithreads
2017-01-09 11:59:53 -05:00
44c0609418
Log annotation warning once if using multithreads
2017-01-08 09:58:40 -05:00
c5df90b598
Merge pull request #1544 from broadinstitute/rhl_thread_safety_1543
...
Synchronize modification/access to practicalAlleleCountForPloidy
2017-01-07 10:00:18 -05:00
4f52395795
Synchronize modification/access to practicalAlleleCountForPloidy
2017-01-06 22:16:35 -05:00
7447616766
Merge pull request #1542 from broadinstitute/rhl_update_stand_call_conf_doc_1538
...
Update stand_call_conf doc string
2017-01-06 20:42:56 -05:00
ab4a9fa64f
Update stand_call_conf doc strings
2017-01-06 17:15:56 -05:00
e86da63d04
Update pom versions to mark the start of GATK 3.8 development
2016-12-12 08:53:23 -05:00
56f2c1ac75
Update pom versions for the 3.7 release
2016-12-12 08:49:43 -05:00
49c1a6c7bd
Merge remote-tracking branch 'unstable/master'
2016-12-12 08:48:29 -05:00
dca24a9fa4
Merge pull request #1533 from broadinstitute/lb_update_jexl_behavior
...
Rev htsjdk + update jexl behavior
2016-12-10 13:33:06 -05:00
5602095a24
Move htsjdk to ver 2.8.1 and picard to ver 2.7.2
...
- Updating VF and tests to match new jexl behavior from htsjdk
- Use Z instead of DP to test behavior on missing annotation
2016-12-10 11:50:30 -05:00
1291cfa881
Merge pull request #1529 from broadinstitute/ms_fs
...
Make Fisher Exact Test match R and GATK4 p-values
2016-12-06 08:55:08 -05:00
24336e85b6
Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz
...
Output filenames with the vcf.gz extension are gzipped, those containing the string ".bcf" result in VCF
2016-12-06 06:46:15 -05:00
172db666d6
Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF"
2016-12-05 22:25:59 -05:00
234ccdf0c3
Merge pull request #1496 from broadinstitute/db_m2_downsampling
...
Expose downsampling parameters as CLI arguments to Mutect2
2016-12-05 21:53:25 -05:00
ca26eee762
Merge pull request #1520 from broadinstitute/gvda_more_docfixes_for_3.7
...
Documentation fixes
2016-12-05 16:59:43 -05:00
3265a664c4
Makes Fisher's exact test match R and GATK4
2016-12-05 16:46:47 -05:00
b1f2301dd3
Add downsampling arguments to Mutect
...
- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
- maxReadsInMemoryPerSample is an activeRegionWalker arg
2016-12-05 14:12:22 -05:00
b42dc1624b
Documentation fixes
...
- Fix missing closing code block tag
- SOR fix + minor fix to template
- Minor typo fixes
- Make no_cmdline_in_header arg visible in docs
- Caveats for UG-only args that are difficult to move out of common collection
- Reference -L and -XL in -gvcf documentation
- Annotation doc fixes (dsde-docs#1289)
- Unhide some ContEst args and make Advanced
- Fix inputPrior error message
- Update web urls
- Add JEXL doc link
2016-12-05 14:09:44 -05:00
66aa735817
Merge pull request #1527 from broadinstitute/rhl_vc_writer_factory_to_builder
...
Replace VariantContextWriterFactory with VariantContextWriterBuilder
2016-11-30 18:12:57 -05:00
68b6f8f638
Replace VariantContextWriterFactory with VariantContextWriterBuilder
2016-11-30 16:04:25 -05:00
7c8f97fdb9
Merge pull request #1522 from broadinstitute/rhl_sam_error_1427
...
Make exit system file type message generic
2016-11-23 11:05:58 -05:00
262c08aee3
Make exit system file type message generic
2016-11-23 10:12:21 -05:00
055d653bc2
Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406
...
Fix adapter bounday for positive strand
2016-11-18 10:25:46 -05:00
196675c0b2
Merge pull request #1354 from broadinstitute/db_issue_1351
...
Fixed logic error in AlleleBalance Annotation. Closes #1351 .
2016-11-16 17:02:31 -05:00
22d94a7096
Fix adapter bounday for positive strand
2016-11-16 16:41:17 -05:00
6156b85ad9
Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample
2016-11-16 14:10:48 -05:00
90f6510cf7
Merge pull request #1516 from broadinstitute/rhl_replace_test_file_1514
...
Change the truth VCF
2016-11-15 16:39:37 -05:00
d61b4c7e91
Change the truth VCF
2016-11-15 14:56:15 -05:00
aac5f55bbe
Merge pull request #1506 from broadinstitute/rhl_set_htsjdk_log_level
...
Set HTSJDK log level
2016-11-15 10:14:17 -05:00
2d06f33227
Set HTSJDK log level
2016-11-15 07:08:19 -05:00
2b19e765d7
Merge pull request #1507 from broadinstitute/gvda_treereduce_vf_#1147
...
Added TreeReduce interface to VariantFiltration
2016-11-14 18:50:36 -05:00
2b83dd7c5b
Added TreeReduce interface to VariantFiltration
2016-11-14 17:19:44 -05:00
a895354a75
Merge pull request #1511 from broadinstitute/rhl_fix_stand_conf_for_calling_1510
...
Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
2016-11-14 15:24:15 -05:00
bcbd7fe952
Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
2016-11-11 02:06:41 -05:00
Ron Levine
Geraldine Van der Auwera
meganshand
David Benjamin