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  • b07c0a6b4c Merge pull request #594 from broadinstitute/dr_vcf_sample_renaming Eric Banks 2014-04-08 11:47:45 -0400
  • af6a897479 Extend on-the-fly sample renaming feature to vcfs David Roazen 2014-04-07 08:42:31 -0400
  • e40cad7b50 Merge pull request #597 from broadinstitute/eb_fix_b36_chainfile Eric Banks 2014-04-08 10:04:44 -0400
  • e690ed1a67 The contig is named MT not M in b36. Delivers PT68890442. Eric Banks 2014-04-08 10:03:47 -0400
  • 85f68f610e Merge pull request #596 from broadinstitute/eb_fix_na12878_roc_curve_maker Eric Banks 2014-04-08 09:56:07 -0400
  • ad336375dc Merge pull request #590 from broadinstitute/vrr_validate_variants_unused_alleles_fix Eric Banks 2014-04-07 22:10:49 -0400
  • 416ccef0c5 Merge pull request #592 from broadinstitute/rp_random_forest_improvements Ryan Poplin 2014-04-07 21:22:45 -0400
  • 5afcc8e05f Change in the command line interface of ValidateVariants. Valentin Ruano-Rubio 2014-04-07 12:22:19 -0400
  • 7d11b4d5f1 Balancing training classes between SNP/Indel and TP/FP. Ryan Poplin 2014-03-12 10:19:16 -0400
  • de2a2442d9 Merge pull request #591 from broadinstitute/rp_add_genotype_summary_annotations Eric Banks 2014-04-07 09:21:07 -0400
  • f058224b3e Adding GenotypeSummaries as INFO field annotations. Ryan Poplin 2014-04-05 10:00:36 -0400
  • d5edb53906 Don't error out with ArithmeticException in ROC maker when using small sets Eric Banks 2014-04-05 23:34:40 -0400
  • 84861fa10a Merge pull request #587 from broadinstitute/eb_actually_fail_on_reduced_bams MauricioCarneiro 2014-04-04 17:27:57 -0400
  • 267603f9a9 Merge pull request #589 from broadinstitute/ldg_SelVarXsampleFile Eric Banks 2014-04-04 15:56:16 -0400
  • ff25b656e1 Added check to make sure file passed in with sample IDs is valid (used in SelectVariants) -- throws UserException. Corresponding test checks for UserException. Laura Gauthier 2014-04-04 15:38:50 -0400
  • 18deeec6b0 Addresses issue with strict validation on GVCF files. Valentin Ruano-Rubio 2014-04-04 10:16:44 -0400
  • 06d78ba068 Expanded documentation to include description of which callsets are being compared in what order and more definitions Laura Gauthier 2014-04-04 10:27:09 -0400
  • 9be07e0838 Merge pull request #588 from broadinstitute/eb_fix_ir_exception Eric Banks 2014-04-04 10:11:51 -0400
  • 7174f8cfeb IndelRealigner throws a user error when it encounters reads with I operators greater than the number of read bases. Eric Banks 2014-04-03 18:16:24 -0400
  • a3d55b3341 Make sure to fail in all cases where the BAM being used was created by ReduceReads. Eric Banks 2014-04-02 21:08:06 -0400
  • 890f4e8873 Merge pull request #586 from broadinstitute/eb_allow_users_to_specify_iupac_sample Geraldine Van der Auwera 2014-04-03 09:29:56 -0400
  • 0b73573abc Slightly modifying the way to use the IUPAC ambiguity codes in the FastaAlternateReferenceMaker. Eric Banks 2014-04-02 21:34:25 -0400
  • 6bba8d7147 Merge pull request #585 from broadinstitute/ks_variantqc_patch Eric Banks 2014-04-02 16:48:42 -0400
  • 0647824e75 Resuscitated from git and copy/pasted in old gsalib methods need for the private script variantCallQC.R to run, for now. Khalid Shakir 2014-04-03 04:20:13 +0800
  • 45c192bb6d Merge pull request #580 from broadinstitute/vrr_graphbase_infinite_likelihoods_reprise Valentin Ruano Rubio 2014-04-02 00:45:17 -0400
  • 84711b8e90 Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) Valentin Ruano-Rubio 2014-03-17 17:13:37 -0400
  • c0286853b7 Merge pull request #584 from broadinstitute/dr_update_queue_test_script_for_naming_change droazen 2014-04-01 11:52:22 -0400
  • ef8f91a5be Update queue test runner script for upcoming naming changes David Roazen 2014-04-01 11:43:10 -0400
  • 8703bd7ad4 Merge pull request #583 from broadinstitute/jt_tabix jmthibault79 2014-03-31 16:17:25 -0400
  • 70fe7f72f1 Return a TabixIndexCreator for appropriate file types [Fixes #68291082] Joel Thibault 2014-03-28 12:00:39 -0400
  • ab5634cbac Test that a Tabix index is created for block-compressed output formats - Replace .idx and .tbi with appropriate constants Joel Thibault 2014-03-27 16:34:30 -0400
  • a2d40c84ba Keep the list of zipped suffixes in sync with Variant Joel Thibault 2014-03-31 13:29:13 -0400
  • a2cd9703fa Rev Picard 1.110.1773 Joel Thibault 2014-03-31 14:02:27 -0400
  • 821fbe7260 Merge pull request #582 from broadinstitute/vrr_hc_bugfixes_dangling_heads Eric Banks 2014-03-31 10:42:08 -0400
  • 313d20d849 Merge pull request #581 from broadinstitute/jt_picard jmthibault79 2014-03-30 11:05:50 -0400
  • 2049eb1658 Rev Picard 1.110.1763 - SamPairUtils migrated in Picard r1737 - Revert IndelRealigner changes made in commit 4f4b85 -- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java -- Picard revision 1723 reverts these changes, so we also revert to match Joel Thibault 2014-03-28 10:39:31 -0400
  • 258b2bce28 Fix loss of key alternative haplotypes due to a change on threading start policy required when recovering dangling heads. Valentin Ruano-Rubio 2014-03-29 17:27:35 -0400
  • 5abb7ea2db Merge pull request #579 from broadinstitute/rp_fix_DP_annotation MauricioCarneiro 2014-03-24 15:49:20 -0400
  • 6566dd6ca9 Fix for dropping of reference sample depth in the DP annotation. -- In the case of hierarchical merge we can't assume that we have only one genotype. -- Removed use of deprecated VC annotation access functions. Ryan Poplin 2014-03-21 13:47:05 -0400
  • c61a791914 Merge pull request #578 from broadinstitute/eb_trivial_fix_to_IR Ryan Poplin 2014-03-21 15:24:58 -0400
  • b8581d7d3a Merge pull request #576 from broadinstitute/rp_fix_AssessNA12878_dropping_contigs Ryan Poplin 2014-03-21 15:23:59 -0400
  • 32a96e3ab3 Fix for reads that are all insertions (e.g. 50I) and causing the IndelRealigner to error out. Eric Banks 2014-03-21 15:01:34 -0400
  • dd1b0a48db Bug fix in AssessNA12878 when working with more than one contig. Ryan Poplin 2014-03-19 16:51:10 -0400
  • 69eaf7c82d Merge pull request #577 from broadinstitute/eb_minor_fixes_for_fragment_utils Ryan Poplin 2014-03-21 14:01:44 -0400
  • ce39fcd8a3 Merge pull request #575 from broadinstitute/eb_various_fixes_for_gvcfs Ryan Poplin 2014-03-21 09:47:08 -0400
  • 0d82a70633 Fixed docs for method and fixed the edge case optimization to properly use equals() on Integers. Eric Banks 2014-03-20 15:55:09 -0400
  • 7c8ce3cd6a Several improvements to GenotypeGVCFs: --includeNonVariantSites now actually works and we propagate AD to hom ref samples Eric Banks 2014-03-20 00:01:50 -0400
  • 824983af1d Enable CombineGVCFs to process gVCFs that were created with basepair resolution. Eric Banks 2014-03-19 19:23:05 -0400
  • 3b1c337401 Have CombineVariants throw a UserError when trying to combine GVCFs from the HaplotypeCaller. Eric Banks 2014-03-19 19:11:40 -0400
  • 7117bebb5e Merge pull request #572 from broadinstitute/rp_fix_manual_reviews_fix Ryan Poplin 2014-03-19 13:58:58 -0400
  • a3aa68e626 Forgot to change the padding ref base as well. Ryan Poplin 2014-03-19 13:58:21 -0400
  • c737b8ed1e Merge pull request #571 from broadinstitute/rp_fix_manual_reviews Ryan Poplin 2014-03-19 13:49:51 -0400
  • 523fd40a07 Fixing the reference base in one of the manual review files. Ryan Poplin 2014-03-19 11:08:06 -0400
  • 3f326b14be Merge pull request #570 from broadinstitute/rp_assessNA12878_arg_docs_fix Ryan Poplin 2014-03-19 09:01:23 -0400
  • 7b38019199 Merge pull request #569 from broadinstitute/vrr_speedup_integration_test droazen 2014-03-18 23:39:16 -0400
  • 905b6066b2 Reduce runtime of very long integration test Valentin Ruano-Rubio 2014-03-18 21:40:14 -0400
  • 14eb0a8a30 Merge pull request #566 from jsilter/master Eric Banks 2014-03-18 15:16:20 -0400
  • cec4ff3a2a Merge pull request #568 from broadinstitute/dr_fix_UtilsUnitTest droazen 2014-03-18 14:31:14 -0400
  • e549f4a9d2 Fix typo in UtilsUnitTest data provider name David Roazen 2014-03-18 11:52:29 -0400
  • a02383fc6a Small argument docs fix in AssessNA12878. Ryan Poplin 2014-03-18 10:07:14 -0400
  • 4ba72d43cf Re-enable GATKRunReportUnitTest David Roazen 2014-03-18 09:53:41 -0400
  • 3cd8158bed Merged bug fix from Stable into Unstable David Roazen 2014-03-18 03:01:28 -0400
  • cfc45fdc0b Disable GATKRunReportUnitTest David Roazen 2014-03-18 02:57:19 -0400
  • afa6abe554 Temporarily disable GATKRunReportUnitTest in unstable while maven issues are worked out David Roazen 2014-03-18 01:28:28 -0400
  • 2d8653f493 Update pom versions to mark the start of GATK 3.2 development David Roazen 2014-03-18 01:18:59 -0400
  • 72492bb875 Merge remote-tracking branch 'unstable/master' David Roazen 2014-03-18 01:11:23 -0400
  • a6a41c777c Update pom versions for 3.1 David Roazen 2014-03-18 01:09:29 -0400
  • 975b3f321e Merge pull request #567 from broadinstitute/dr_public_GATKRunReport_tests droazen 2014-03-17 18:33:26 -0400
  • d5e38ec39b Move GATKRunReport tests from private to public David Roazen 2014-03-17 18:13:08 -0400
  • 6b3320f067 Merge pull request #561 from broadinstitute/ks_package_classpath droazen 2014-03-17 17:38:24 -0400
  • 0715a9fd7d Make sure to follow HTTP redirects when loading dbSpec Jacob Silterra 2014-03-17 16:31:14 -0400
  • cfc4f708dc Load dbSpec into string before parsing it as JSON Jacob Silterra 2014-03-17 16:30:26 -0400
  • 2e34ff7692 Merge pull request #563 from broadinstitute/aw_refactor_tribble Eric Banks 2014-03-17 13:35:46 -0400
  • 2115195d18 Merge pull request #565 from broadinstitute/eb_remove_one_more_reference_to_rr Eric Banks 2014-03-17 12:29:26 -0400
  • dabdd0a0fd Remove unused and unnecessary argument Eric Banks 2014-03-17 12:28:27 -0400
  • 759c4c8c5a Merge pull request #564 from broadinstitute/eb_rename_truth_set Eric Banks 2014-03-17 12:15:57 -0400
  • b9b2dcc712 Mark had mis-named this input callset to the knowledgebase. It's the pilot2 liftover, not pilot1. Eric Banks 2014-03-17 12:14:29 -0400
  • 0369f93b24 GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). Alec Wysoker 2014-02-26 16:59:03 -0500
  • 34c697bf12 Merge pull request #554 from broadinstitute/bh_SOR_new_annotation Eric Banks 2014-03-17 10:58:13 -0400
  • bb4a7bf87e Merge pull request #562 from broadinstitute/ldg_newCGPdocs Eric Banks 2014-03-17 10:39:20 -0400
  • 40c13d446a Added documentation category for CalculateGenotypePosteriors Laura Gauthier 2014-03-17 08:48:48 -0400
  • c1b4390691 Merge pull request #559 from broadinstitute/vrr_assembly_graph_edge_info_revise Ryan Poplin 2014-03-17 09:27:19 -0400
  • 639247ab48 Updated package-tests classpath, and allowing javac -cp <package>.jar. Package tests now hard coding just the gatk-framework tests jar, to include ONLY BaseTest, until the exclusions may be debugged. Removing cofoja's annotation service from the package jars, to allow javac -cp <package>.jar. Khalid Shakir 2014-03-17 05:47:59 -0400
  • 2e964c59b4 Improved criteria to select best haplotypes out from the assembly graph. Valentin Ruano-Rubio 2014-03-07 13:05:06 -0500
  • 82108d110f New abstract class StrandBiasTest() with old sub-class FisherStrand() and new sub-class StrandOddsRatio(). Latter is test based on symmetric odds ratio more appropriate than Fisher exact test when number of samples is large. https://www.pivotaltracker.com/story/show/66087886 Bertrand Haas 2014-03-14 10:41:41 -0400
  • a0c252f084 Merge pull request #560 from broadinstitute/dr_fix_phone_home_packaging_error Eric Banks 2014-03-14 11:54:30 -0400
  • 1324120c17 Unconditionally include all of commons-httpclient in the GATK/Queue jars David Roazen 2014-03-14 10:50:15 -0400
  • 7c7ff90266 Merge pull request #558 from broadinstitute/rp_vqsr_nondeterminism_fix Eric Banks 2014-03-12 14:35:51 -0400
  • d3a4b57491 Merge pull request #556 from broadinstitute/eb_use_iupac_in_FARM Eric Banks 2014-03-12 14:33:06 -0400
  • ffaf92f871 Added new functionality to the FastaAlternateReferenceMaker to have it output IUPAC codes for het sites. Eric Banks 2014-03-11 23:43:56 -0400
  • 907d1d6160 Fix for non-determinism in the VQSR with very large data sets Ryan Poplin 2014-03-12 10:25:12 -0400
  • 4e74e77e74 Merge pull request #555 from broadinstitute/eb_add_option_to_CGVCFs_for_all_sites_GVCF ldgauthier 2014-03-12 10:01:18 -0400
  • 1f6b761c7d Merge pull request #557 from broadinstitute/dr_add_warning_for_intel_pairhmm Eric Banks 2014-03-12 09:59:32 -0400
  • c67ced5f3b Emit a warning whenever the VectorLoglessPairHMM is used David Roazen 2014-03-12 09:55:35 -0400
  • d697e0144f Added an option to CombineGVCFs to create basepair resolution gVCFs from banded ones. Eric Banks 2014-03-12 01:32:51 -0400
  • 35aa24ab54 Merge pull request #552 from broadinstitute/rp_HaplotypeCaller_1kg_consensus_mode Ryan Poplin 2014-03-11 11:17:30 -0400
  • 34d11fe40c Added the consensus mode used for the 1000 Genomes Project to the HaplotypeCaller. Ryan Poplin 2014-01-28 09:11:44 -0500
  • 8b53567dc7 Merge pull request #553 from broadinstitute/dr_rename_pipeline_tests droazen 2014-03-10 21:36:45 -0400
  • 78562c14bb Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests David Roazen 2014-03-10 15:20:47 -0400
  • d0501d0083 Merge pull request #547 from broadinstitute/intel_pairhmm droazen 2014-03-10 15:27:20 -0400