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14385 Commits (a72be69062b178bad20441df4a4e18bf32cc8ef3)

Author SHA1 Message Date
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
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
Ron Levine f6c18a5182 Throw an exception if the BQSR input covariants file is not found 2016-08-11 12:46:14 -04:00
Peter Fan 3510906c7f addresses issue #1280 now interval padding works for exclude intervals 2016-08-10 13:45:45 -04:00
samuelklee 7959324f08 Merge pull request #1451 from broadinstitute/sl_issue_1345_fix_2 
Changed maximum allowed GQB value to 100.
 2016-08-05 15:12:20 -04:00
Samuel Lee 49507faaa3 Changed maximum allowed GQB value to 100. 2016-08-05 13:06:31 -04:00
Ron Levine 0630c7befd Merge pull request #1423 from broadinstitute/rhl_read_sra 
Added support for directly reading SRA runs
 2016-08-02 18:10:33 -04:00
Andrii Nikitiuk a465c87ff8 Added support for directly reading SRA runs 2016-08-02 15:21:14 -04:00
samuelklee 6bca5a060f Merge pull request #1446 from broadinstitute/sl_issue_1345_fix 
Fixed MD5 broken by PR #1440.
 2016-07-27 21:53:00 -04:00
Samuel Lee 832a383acd Fixed MD5 broken by PR #1440. 2016-07-27 13:51:20 -04:00
samuelklee 9a6ce7a347 Merge pull request #1440 from broadinstitute/sl_issue_1345 
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
 2016-07-26 14:55:59 -04:00
Valentin Ruano Rubio e194b52ef3 Merge pull request #1442 from broadinstitute/vrr_genotype_gvcf_performance_fix 
GenotypeGVCFs performance and QUAL miscalculation fix applied to master.
 2016-07-26 13:13:52 -04:00
Valentin Ruano Rubio fef63ce6a8 Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization. 
Addresses issue #1439 (thus #1437).

Fixes a bug where non informative PLs were not handled appropriatelly when calculating multi-allelic site QUAL values.
This was resulting in long execution times for very large datasets (~200,000 samples in the case of ExAC2).
 2016-07-25 17:19:03 -04:00
Samuel Lee 3daed9e5a1 Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests. 2016-07-20 16:48:59 -04:00
Ron Levine b4eb479727 Merge pull request #1417 from broadinstitute/rhl_ggvcf_span_del 
Removed spanning deletions if the deletion was removed
 2016-07-19 16:55:06 -04:00
Ron Levine 7392c4d1b0 Removed spanning deletions if the deletion was removed 2016-07-19 12:23:49 -04:00