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14399 Commits (bcbd7fe952edf6ccee822c8401339dfe702a77ec)

Author SHA1 Message Date
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
Ron Levine 956b18fbb7 Make ReadPosRankSumTest.isUsableRead() account for deletions 2016-09-07 13:52:09 -04:00
Steve Huang 3c88e6859f fix 1430 for genotype filters; refactored filter() method; added unit and integration test; more comprehensive fix must be done first on htsjdk side in JEXLMap (#1456) 2016-09-06 17:30:18 -04:00
David Benjamin d582ee6d3c Merge pull request #1463 from broadinstitute/db_m2 
More Mutect2 refactoring
 2016-08-31 15:46:46 -04:00
David Benjamin 601c26a592 More small refactorings of Mutect2 code 2016-08-29 12:45:13 -04:00
Ron Levine 814ad21006 Merge pull request #1454 from broadinstitute/rrhl_rm_stand_emit_conf 
Remove -stand_emit_conf argument
 2016-08-27 08:57:09 -04:00
Ron Levine a883905101 Remove -stand_emit_conf argument 2016-08-26 22:09:11 -04:00
Takuto Sato cb0dedeb49 Merge pull request #1462 from broadinstitute/ts_m2_refactor 
Clean up SomaticGenotypingEngine::callMutations and add TODOs
 2016-08-26 14:15:33 -04:00
Takuto Sato bc3b3ac0ec Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs. 2016-08-26 14:12:05 -04:00
David Benjamin 4aede99697 Merge pull request #1453 from broadinstitute/db_mutect2 
Lots of small improvements to Mutect2 code
 2016-08-23 18:35:38 -04:00
Ron Levine 53e1d42d28 Merge pull request #1460 from broadinstitute/rhl_rank_sum_test_del_return 
Make getElementForRead() in RankSumTest robust
 2016-08-23 16:36:30 -04:00
Ron Levine cd5c04f806 Make getElementForRead() in RankSumTest robust 2016-08-23 14:56:32 -04:00
David Benjamin 01142dfb1c Lots of small improvements to Mutect2 code 2016-08-23 09:50:48 -04:00
Ron Levine ebceb06284 Merge pull request #1445 from broadinstitute/rhl_read_pos_span_del 
Ignore spanning deletions in Rank Sum tests
 2016-08-17 20:21:47 -04:00
Ron Levine abc4d5b7b3 Bypass spanning deletions in Rank Sum tests 2016-08-17 14:02:22 -04:00
Peter Fan 01fdb90096 Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding 
addresses issue #1280 now interval padding works for exclude intervals
 2016-08-17 13:15:15 -04:00
Ron Levine 27e56b2bb9 Merge pull request #1441 from broadinstitute/rhl_printreads_bqsr_fail 
Throw an exception if the BQSR input covariants file is not found
 2016-08-11 16:16:08 -04:00