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14415 Commits (b42dc1624b3b518dc404870df6feb8347c9e74f6)

Author SHA1 Message Date
Geraldine Van der Auwera 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
Ron Levine 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
Ron Levine 68b6f8f638 Replace VariantContextWriterFactory with VariantContextWriterBuilder 2016-11-30 16:04:25 -05:00
Ron Levine 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
Ron Levine 262c08aee3 Make exit system file type message generic 2016-11-23 10:12:21 -05:00
David Benjamin 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
Ron Levine 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
Ron Levine 22d94a7096 Fix adapter bounday for positive strand 2016-11-16 16:41:17 -05:00
David Benjamin 6156b85ad9 Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample 2016-11-16 14:10:48 -05:00
Ron Levine 90f6510cf7 Merge pull request #1516 from broadinstitute/rhl_replace_test_file_1514 
Change the truth VCF
 2016-11-15 16:39:37 -05:00
Ron Levine d61b4c7e91 Change the truth VCF 2016-11-15 14:56:15 -05:00
Ron Levine aac5f55bbe Merge pull request #1506 from broadinstitute/rhl_set_htsjdk_log_level 
Set HTSJDK log level
 2016-11-15 10:14:17 -05:00
Ron Levine 2d06f33227 Set HTSJDK log level 2016-11-15 07:08:19 -05:00
Ron Levine 2b19e765d7 Merge pull request #1507 from broadinstitute/gvda_treereduce_vf_#1147 
Added TreeReduce interface to VariantFiltration
 2016-11-14 18:50:36 -05:00
Geraldine Van der Auwera 2b83dd7c5b Added TreeReduce interface to VariantFiltration 2016-11-14 17:19:44 -05:00
Geraldine Van der Auwera 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
Ron Levine bcbd7fe952 Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10 2016-11-11 02:06:41 -05:00
Ron Levine 94fe2aabbd Merge pull request #1494 from broadinstitute/rhl_bcs_pos_1493 
BaseCountsBySample counting bases at a particular position
 2016-11-08 15:00:00 -05:00
Ron Levine df0ba2ce8d BaseCountsBySample counting bases at a particular position 2016-11-08 13:31:05 -05:00
Valentin Ruano Rubio 40ae430a70 Merge pull request #1502 from broadinstitute/db_port_qual_tweaking 
Backport numerics changes in new qual
 2016-11-01 10:26:26 -04:00
David Benjamin 029632eb1c backport numerics changes in new qual 2016-11-01 03:16:21 -04:00
Steve Huang 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
Valentin Ruano Rubio 26d033d725 Merge pull request #1498 from broadinstitute/rhl_warn_to_stderr_1497 
Write saved WARN messages to stderr instead of stdout
 2016-10-24 17:01:37 -04:00
Ron Levine d7090ef158 Write saved WARN messages to stderr instead of stdout 2016-10-21 13:01:07 -04:00
Ron Levine 0d2a3e754c Merge pull request #1490 from broadinstitute/rhl_ggvcf_hom_ref_high_mq 
Remove RankSumTest and RMSAnnotation from hom-ref sites
 2016-10-14 14:41:49 -04:00
Ron Levine bd6d050187 Merge pull request #1485 from broadinstitute/rhl_mv_samfilereader_samreaderfactory 
Replace SAMFileReader with calls to SamReaderFactory
 2016-10-14 12:52:12 -04:00
Ron Levine 01a858542f Remove RankSumTest and RMSAnnotation from hom-ref sites 2016-10-14 11:34:54 -04:00
Ron Levine cfd3ffa2c0 Replace SAMFileReader with calls to SamReaderFactory 2016-10-14 11:22:54 -04:00
Valentin Ruano Rubio 2ee0755c35 Merge pull request #1492 from broadinstitute/vrr_newqual_nan_fix 
Fixes NaN issue in new Qual calculator
 2016-10-11 23:31:19 -04:00
Ron Levine a72be69062 Merge pull request #1488 from broadinstitute/rhl_dup_col_rld 
Add read group identifier to column names
 2016-10-11 18:40:40 -04:00
Pierre Lindenbaum a301ba1977 Add read group identifier to column names 
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
Valentin Ruano Rubio 16417bbf34 Fixes NaN issue in new Qual calculator 
Fixes issue #1491
 2016-10-11 16:03:06 -04:00
Ron Levine 967b4f4ae8 Merge pull request #1487 from broadinstitute/rhl_deprecate_strand_emit_conf 
Resurrect and deprecate -stand_emit_conf
 2016-10-09 12:56:50 -04:00
Ron Levine 81a9ece45b deprecate -stand_emit_conf 2016-10-09 10:24:09 -04:00
Ron Levine 7b3af3820e Merge pull request #1483 from broadinstitute/rhl_fix_unit_tests 
Remove sra group
 2016-09-26 08:20:24 -04:00
Ron Levine 2c83081560 Remove sra group 2016-09-23 17:39:10 -04:00
Ron Levine 6bfdaa37c3 Merge pull request #1480 from broadinstitute/rhl_farm_wrong_ambig_code_star_allele 
Assign correct ambiguity code for * allele
 2016-09-22 13:03:04 -04:00
Ron Levine 4ef396f72e Assign correct ambiguity code for * allele 2016-09-22 11:02:44 -04:00
David Benjamin 3b90b9c7de Merge pull request #1481 from broadinstitute/db_backport_qual 
Backport of AlleleFrequencyCalculator aka the new QUAL
 2016-09-21 19:54:23 -04:00
David Benjamin 318bee2269 Backport new AFCalculator 2016-09-21 15:21:56 -04:00
Ron Levine 7b74dc1634 Merge pull request #1478 from broadinstitute/rhl_htsjdk_2.6.1_picard_2.6.0 
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
 2016-09-19 13:17:34 -04:00
Ron Levine c13e3752d6 Move htsjdk to ver 2.6.1 and picard to ver 2.6.0 2016-09-16 16:36:52 -04:00
Ron Levine e0cf6d1985 Merge pull request #1470 from broadinstitute/rhl_rm_nonref_genotypegvcfs 
Remove NON_REF from allSites VCF output
 2016-09-16 16:31:13 -04:00
Ron Levine 6564066de3 Remove NON_REF from allSites VCF output 2016-09-16 13:55:52 -04:00
Steve Huang 091d05370b Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices (#1475) 
* 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 f51d20c517 Merge pull request #1469 from broadinstitute/rhl_upgrade_apache_collections_to_v3.2.2 
Upgrade Apache Commons Collections to version 3.2.2
 2016-09-09 12:57:09 -04:00
Ron Levine 227038d0f8 Merge pull request #1471 from broadinstitute/rhl_rm_gvcf_blocks_genotype_gvcf 
Do not emit GVCF block definitions in the header
 2016-09-09 10:00:15 -04:00
Ron Levine a7b1130224 Do not emit GVCF block definitions in the header 2016-09-09 07:41:03 -04:00
Ron Levine e84359a02e Merge pull request #1467 from broadinstitute/rhl_fix_rprst_is_usable 
Make ReadPosRankSumTest.isUsableRead() account for deletions
 2016-09-08 11:52:54 -04:00
Ron Levine ab454e8812 Upgrade Apache Commons Collections to version 3.2.2 2016-09-07 18:59:21 -04:00