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  • 1f6645539a Make upstreamDeletionsLoc ThreadLocal Ron Levine 2017-01-11 17:58:20 -0500
  • f092e1438d Allow disabling of BadMateFilter in HaplotypeCaller Ron Levine 2017-01-06 09:19:21 -0500
  • bb87730ddc Merge pull request #1546 from broadinstitute/rhl_annot_warn_1540 Ron Levine 2017-01-09 11:59:53 -0500
  • 44c0609418 Log annotation warning once if using multithreads Ron Levine 2017-01-06 17:00:29 -0500
  • c5df90b598 Merge pull request #1544 from broadinstitute/rhl_thread_safety_1543 Ron Levine 2017-01-07 10:00:18 -0500
  • 4f52395795 Synchronize modification/access to practicalAlleleCountForPloidy Ron Levine 2017-01-06 22:16:35 -0500
  • 7447616766 Merge pull request #1542 from broadinstitute/rhl_update_stand_call_conf_doc_1538 Ron Levine 2017-01-06 20:42:56 -0500
  • ab4a9fa64f Update stand_call_conf doc strings Ron Levine 2017-01-06 17:15:56 -0500
  • e86da63d04 Update pom versions to mark the start of GATK 3.8 development Geraldine Van der Auwera 2016-12-12 08:53:23 -0500
  • 56f2c1ac75 Update pom versions for the 3.7 release Geraldine Van der Auwera 2016-12-12 08:49:43 -0500
  • 49c1a6c7bd Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2016-12-12 08:48:29 -0500
  • dca24a9fa4 Merge pull request #1533 from broadinstitute/lb_update_jexl_behavior Geraldine Van der Auwera 2016-12-10 13:33:06 -0500
  • 5602095a24 Move htsjdk to ver 2.8.1 and picard to ver 2.7.2 Ron Levine 2016-12-07 15:17:20 -0500
  • 1291cfa881 Merge pull request #1529 from broadinstitute/ms_fs meganshand 2016-12-06 08:55:08 -0500
  • 24336e85b6 Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz Ron Levine 2016-12-06 06:46:15 -0500
  • 172db666d6 Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF" Ron Levine 2016-12-01 20:50:59 -0500
  • 234ccdf0c3 Merge pull request #1496 from broadinstitute/db_m2_downsampling Geraldine Van der Auwera 2016-12-05 21:53:25 -0500
  • ca26eee762 Merge pull request #1520 from broadinstitute/gvda_more_docfixes_for_3.7 Geraldine Van der Auwera 2016-12-05 16:59:43 -0500
  • 3265a664c4 Makes Fisher's exact test match R and GATK4 meganshand 2016-12-02 16:44:14 -0500
  • b1f2301dd3 Add downsampling arguments to Mutect David Benjamin 2016-10-19 14:16:14 -0400
  • b42dc1624b Documentation fixes Geraldine Van der Auwera 2016-06-04 02:14:49 -0400
  • 66aa735817 Merge pull request #1527 from broadinstitute/rhl_vc_writer_factory_to_builder Ron Levine 2016-11-30 18:12:57 -0500
  • 68b6f8f638 Replace VariantContextWriterFactory with VariantContextWriterBuilder Ron Levine 2016-11-28 21:01:47 -0500
  • 7c8f97fdb9 Merge pull request #1522 from broadinstitute/rhl_sam_error_1427 Ron Levine 2016-11-23 11:05:58 -0500
  • 262c08aee3 Make exit system file type message generic Ron Levine 2016-11-23 01:06:13 -0500
  • 055d653bc2 Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406 David Benjamin 2016-11-18 10:25:46 -0500
  • 196675c0b2 Merge pull request #1354 from broadinstitute/db_issue_1351 Ron Levine 2016-11-16 17:02:31 -0500
  • 22d94a7096 Fix adapter bounday for positive strand Ron Levine 2016-11-14 12:03:54 -0500
  • 6156b85ad9 Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample David Benjamin 2016-04-25 15:28:22 -0400
  • 90f6510cf7 Merge pull request #1516 from broadinstitute/rhl_replace_test_file_1514 Ron Levine 2016-11-15 16:39:37 -0500
  • d61b4c7e91 Change the truth VCF Ron Levine 2016-11-15 14:56:15 -0500
  • aac5f55bbe Merge pull request #1506 from broadinstitute/rhl_set_htsjdk_log_level Ron Levine 2016-11-15 10:14:17 -0500
  • 2d06f33227 Set HTSJDK log level Ron Levine 2016-11-08 14:35:03 -0500
  • 2b19e765d7 Merge pull request #1507 from broadinstitute/gvda_treereduce_vf_#1147 Ron Levine 2016-11-14 18:50:36 -0500
  • 2b83dd7c5b Added TreeReduce interface to VariantFiltration Geraldine Van der Auwera 2015-09-28 17:34:00 -0400
  • a895354a75 Merge pull request #1511 from broadinstitute/rhl_fix_stand_conf_for_calling_1510 Geraldine Van der Auwera 2016-11-14 15:24:15 -0500
  • bcbd7fe952 Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10 Ron Levine 2016-11-10 16:53:13 -0500
  • 94fe2aabbd Merge pull request #1494 from broadinstitute/rhl_bcs_pos_1493 Ron Levine 2016-11-08 15:00:00 -0500
  • df0ba2ce8d BaseCountsBySample counting bases at a particular position Ron Levine 2016-10-17 10:09:51 -0400
  • 40ae430a70 Merge pull request #1502 from broadinstitute/db_port_qual_tweaking Valentin Ruano Rubio 2016-11-01 10:26:26 -0400
  • 029632eb1c backport numerics changes in new qual David Benjamin 2016-11-01 03:16:21 -0400
  • cc91052e69 fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count; added hackish integration test (#1457) Steve Huang 2016-10-27 11:19:49 -0400
  • 26d033d725 Merge pull request #1498 from broadinstitute/rhl_warn_to_stderr_1497 Valentin Ruano Rubio 2016-10-24 17:01:37 -0400
  • d7090ef158 Write saved WARN messages to stderr instead of stdout Ron Levine 2016-10-21 13:01:07 -0400
  • 0d2a3e754c Merge pull request #1490 from broadinstitute/rhl_ggvcf_hom_ref_high_mq Ron Levine 2016-10-14 14:41:49 -0400
  • bd6d050187 Merge pull request #1485 from broadinstitute/rhl_mv_samfilereader_samreaderfactory Ron Levine 2016-10-14 12:52:12 -0400
  • 01a858542f Remove RankSumTest and RMSAnnotation from hom-ref sites Ron Levine 2016-10-07 12:10:28 -0400
  • cfd3ffa2c0 Replace SAMFileReader with calls to SamReaderFactory Ron Levine 2016-09-20 12:49:06 -0400
  • 2ee0755c35 Merge pull request #1492 from broadinstitute/vrr_newqual_nan_fix Valentin Ruano Rubio 2016-10-11 23:31:19 -0400
  • a72be69062 Merge pull request #1488 from broadinstitute/rhl_dup_col_rld Ron Levine 2016-10-11 18:40:40 -0400
  • a301ba1977 Add read group identifier to column names Pierre Lindenbaum 2016-09-23 11:17:24 +0200
  • 16417bbf34 Fixes NaN issue in new Qual calculator Valentin Ruano Rubio 2016-10-11 11:54:17 -0400
  • 967b4f4ae8 Merge pull request #1487 from broadinstitute/rhl_deprecate_strand_emit_conf Ron Levine 2016-10-09 12:56:50 -0400
  • 81a9ece45b deprecate -stand_emit_conf Ron Levine 2016-10-02 12:13:18 -0400
  • 7b3af3820e Merge pull request #1483 from broadinstitute/rhl_fix_unit_tests Ron Levine 2016-09-26 08:20:24 -0400
  • 2c83081560 Remove sra group Ron Levine 2016-09-23 17:39:10 -0400
  • 6bfdaa37c3 Merge pull request #1480 from broadinstitute/rhl_farm_wrong_ambig_code_star_allele Ron Levine 2016-09-22 13:03:04 -0400
  • 4ef396f72e Assign correct ambiguity code for * allele Ron Levine 2016-09-09 14:20:18 -0400
  • 3b90b9c7de Merge pull request #1481 from broadinstitute/db_backport_qual David Benjamin 2016-09-21 19:54:23 -0400
  • 318bee2269 Backport new AFCalculator David Benjamin 2016-08-26 14:05:49 -0400
  • 7b74dc1634 Merge pull request #1478 from broadinstitute/rhl_htsjdk_2.6.1_picard_2.6.0 Ron Levine 2016-09-19 13:17:34 -0400
  • c13e3752d6 Move htsjdk to ver 2.6.1 and picard to ver 2.6.0 Ron Levine 2016-09-16 11:30:07 -0400
  • e0cf6d1985 Merge pull request #1470 from broadinstitute/rhl_rm_nonref_genotypegvcfs Ron Levine 2016-09-16 16:31:13 -0400
  • 6564066de3 Remove NON_REF from allSites VCF output Ron Levine 2016-09-06 18:57:42 -0400
  • 091d05370b Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices (#1475) Steve Huang 2016-09-13 21:20:44 -0400
  • f51d20c517 Merge pull request #1469 from broadinstitute/rhl_upgrade_apache_collections_to_v3.2.2 Ron Levine 2016-09-09 12:57:09 -0400
  • 227038d0f8 Merge pull request #1471 from broadinstitute/rhl_rm_gvcf_blocks_genotype_gvcf Ron Levine 2016-09-09 10:00:15 -0400
  • a7b1130224 Do not emit GVCF block definitions in the header Ron Levine 2016-09-08 16:21:32 -0400
  • e84359a02e Merge pull request #1467 from broadinstitute/rhl_fix_rprst_is_usable Ron Levine 2016-09-08 11:52:54 -0400
  • ab454e8812 Upgrade Apache Commons Collections to version 3.2.2 Ron Levine 2016-09-06 18:57:42 -0400
  • 956b18fbb7 Make ReadPosRankSumTest.isUsableRead() account for deletions Ron Levine 2016-09-06 10:49:20 -0400
  • 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) Steve Huang 2016-09-06 17:30:18 -0400
  • d582ee6d3c Merge pull request #1463 from broadinstitute/db_m2 David Benjamin 2016-08-31 15:46:46 -0400
  • 601c26a592 More small refactorings of Mutect2 code David Benjamin 2016-08-25 11:54:02 -0400
  • 814ad21006 Merge pull request #1454 from broadinstitute/rrhl_rm_stand_emit_conf Ron Levine 2016-08-27 08:57:09 -0400
  • a883905101 Remove -stand_emit_conf argument Ron Levine 2016-08-17 10:31:59 -0400
  • cb0dedeb49 Merge pull request #1462 from broadinstitute/ts_m2_refactor Takuto Sato 2016-08-26 14:15:33 -0400
  • bc3b3ac0ec Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs. Takuto Sato 2016-08-25 13:20:13 -0400
  • 4aede99697 Merge pull request #1453 from broadinstitute/db_mutect2 David Benjamin 2016-08-23 18:35:38 -0400
  • 53e1d42d28 Merge pull request #1460 from broadinstitute/rhl_rank_sum_test_del_return Ron Levine 2016-08-23 16:36:30 -0400
  • cd5c04f806 Make getElementForRead() in RankSumTest robust Ron Levine 2016-08-19 14:29:33 -0400
  • 01142dfb1c Lots of small improvements to Mutect2 code David Benjamin 2016-08-04 01:50:13 -0400
  • ebceb06284 Merge pull request #1445 from broadinstitute/rhl_read_pos_span_del Ron Levine 2016-08-17 20:21:47 -0400
  • abc4d5b7b3 Bypass spanning deletions in Rank Sum tests Ron Levine 2016-07-26 12:55:14 -0400
  • 01fdb90096 Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding Peter Fan 2016-08-17 13:15:15 -0400
  • 27e56b2bb9 Merge pull request #1441 from broadinstitute/rhl_printreads_bqsr_fail Ron Levine 2016-08-11 16:16:08 -0400
  • f6c18a5182 Throw an exception if the BQSR input covariants file is not found Ron Levine 2016-07-21 13:29:36 -0400
  • 3510906c7f addresses issue #1280 now interval padding works for exclude intervals Peter Fan 2016-08-03 14:03:05 -0400
  • 7959324f08 Merge pull request #1451 from broadinstitute/sl_issue_1345_fix_2 samuelklee 2016-08-05 15:12:20 -0400
  • 49507faaa3 Changed maximum allowed GQB value to 100. Samuel Lee 2016-08-02 15:48:19 -0400
  • 0630c7befd Merge pull request #1423 from broadinstitute/rhl_read_sra Ron Levine 2016-08-02 18:10:33 -0400
  • a465c87ff8 Added support for directly reading SRA runs Andrii Nikitiuk 2015-09-15 17:15:49 -0400
  • 6bca5a060f Merge pull request #1446 from broadinstitute/sl_issue_1345_fix samuelklee 2016-07-27 21:53:00 -0400
  • 832a383acd Fixed MD5 broken by PR #1440. Samuel Lee 2016-07-27 13:44:12 -0400
  • 9a6ce7a347 Merge pull request #1440 from broadinstitute/sl_issue_1345 samuelklee 2016-07-26 14:55:59 -0400
  • e194b52ef3 Merge pull request #1442 from broadinstitute/vrr_genotype_gvcf_performance_fix Valentin Ruano Rubio 2016-07-26 13:13:52 -0400
  • fef63ce6a8 Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization. Valentin Ruano Rubio 2016-07-15 14:20:52 -0400
  • 3daed9e5a1 Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests. Samuel Lee 2016-07-19 14:44:49 -0400
  • b4eb479727 Merge pull request #1417 from broadinstitute/rhl_ggvcf_span_del Ron Levine 2016-07-19 16:55:06 -0400
  • 7392c4d1b0 Removed spanning deletions if the deletion was removed Ron Levine 2016-06-23 17:14:06 -0400