24336e85b6
Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz
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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
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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
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Documentation fixes
2016-12-05 16:59:43 -05:00
b1f2301dd3
Add downsampling arguments to Mutect
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- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
- maxReadsInMemoryPerSample is an activeRegionWalker arg
2016-12-05 14:12:22 -05:00
b42dc1624b
Documentation fixes
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- 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
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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
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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
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Fix adapter bounday for positive strand
2016-11-18 10:25:46 -05:00
196675c0b2
Merge pull request #1354 from broadinstitute/db_issue_1351
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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
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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
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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
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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
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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
94fe2aabbd
Merge pull request #1494 from broadinstitute/rhl_bcs_pos_1493
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BaseCountsBySample counting bases at a particular position
2016-11-08 15:00:00 -05:00
df0ba2ce8d
BaseCountsBySample counting bases at a particular position
2016-11-08 13:31:05 -05:00
40ae430a70
Merge pull request #1502 from broadinstitute/db_port_qual_tweaking
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Backport numerics changes in new qual
2016-11-01 10:26:26 -04:00
029632eb1c
backport numerics changes in new qual
2016-11-01 03:16:21 -04:00
cc91052e69
fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count; added hackish integration test ( #1457 )
2016-10-27 11:19:49 -04:00
26d033d725
Merge pull request #1498 from broadinstitute/rhl_warn_to_stderr_1497
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Write saved WARN messages to stderr instead of stdout
2016-10-24 17:01:37 -04:00
d7090ef158
Write saved WARN messages to stderr instead of stdout
2016-10-21 13:01:07 -04:00
0d2a3e754c
Merge pull request #1490 from broadinstitute/rhl_ggvcf_hom_ref_high_mq
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Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 14:41:49 -04:00
bd6d050187
Merge pull request #1485 from broadinstitute/rhl_mv_samfilereader_samreaderfactory
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Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 12:52:12 -04:00
01a858542f
Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 11:34:54 -04:00
cfd3ffa2c0
Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 11:22:54 -04:00
2ee0755c35
Merge pull request #1492 from broadinstitute/vrr_newqual_nan_fix
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Fixes NaN issue in new Qual calculator
2016-10-11 23:31:19 -04:00
a72be69062
Merge pull request #1488 from broadinstitute/rhl_dup_col_rld
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Add read group identifier to column names
2016-10-11 18:40:40 -04:00
a301ba1977
Add read group identifier to column names
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If two SAMReadGroupRecords share the same sample name, the output will contain duplicate column headers.
This PR fix the problem.
2016-10-11 18:37:11 -04:00
16417bbf34
Fixes NaN issue in new Qual calculator
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Fixes issue #1491
2016-10-11 16:03:06 -04:00
967b4f4ae8
Merge pull request #1487 from broadinstitute/rhl_deprecate_strand_emit_conf
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Resurrect and deprecate -stand_emit_conf
2016-10-09 12:56:50 -04:00
81a9ece45b
deprecate -stand_emit_conf
2016-10-09 10:24:09 -04:00
7b3af3820e
Merge pull request #1483 from broadinstitute/rhl_fix_unit_tests
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Remove sra group
2016-09-26 08:20:24 -04:00
2c83081560
Remove sra group
2016-09-23 17:39:10 -04:00
6bfdaa37c3
Merge pull request #1480 from broadinstitute/rhl_farm_wrong_ambig_code_star_allele
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Assign correct ambiguity code for * allele
2016-09-22 13:03:04 -04:00
4ef396f72e
Assign correct ambiguity code for * allele
2016-09-22 11:02:44 -04:00
3b90b9c7de
Merge pull request #1481 from broadinstitute/db_backport_qual
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Backport of AlleleFrequencyCalculator aka the new QUAL
2016-09-21 19:54:23 -04:00
318bee2269
Backport new AFCalculator
2016-09-21 15:21:56 -04:00
7b74dc1634
Merge pull request #1478 from broadinstitute/rhl_htsjdk_2.6.1_picard_2.6.0
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Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-19 13:17:34 -04:00
c13e3752d6
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-16 16:36:52 -04:00
e0cf6d1985
Merge pull request #1470 from broadinstitute/rhl_rm_nonref_genotypegvcfs
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Remove NON_REF from allSites VCF output
2016-09-16 16:31:13 -04:00
6564066de3
Remove NON_REF from allSites VCF output
2016-09-16 13:55:52 -04:00
091d05370b
Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices ( #1475 )
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* alt alle removal by likelihoods now robust to ref allele indices (no longer assumes 0-indexed ref)
2016-09-13 21:20:44 -04:00
Ron Levine
Geraldine Van der Auwera
David Benjamin
Valentin Ruano Rubio
Steve Huang
Pierre Lindenbaum