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  • f8ad91b16f Reverting a bunch of bad -B type drops Mark DePristo 2011-08-08 16:57:38 -0400
  • 5e288136e0 Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself. David Roazen 2011-08-08 16:51:43 -0400
  • f0ee789a99 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-08 16:25:43 -0400
  • d7813db217 Combine Variants was actually outputting invalid VCFs in cases where it was combining Variant Contexts with different alternate alleles: if any of the genotypes had PLs they were no longer valid/correct. Added a check for such cases (the combined VC has more alleles than an original VC) and strip out the PLs when triggered; added integration test to cover it. I also added the check to Select Variants, although it currently doesn't remove unused alleles so it should never trigger. Is there any reason not to strip out unused alleles after a select? Eric Banks 2011-08-08 16:25:35 -0400
  • 383bb6f0e0 Merge branch 'master' into rodRefactor Mark DePristo 2011-08-08 15:25:55 -0400
  • 4f8fc0f2f1 VCF3 now dynamically determined Mark DePristo 2011-08-08 15:05:47 -0400
  • ba7353c561 Updated IntegrationTests to use the new type free format for VCF files Mark DePristo 2011-08-08 15:04:38 -0400
  • 0810c42309 GATK now does dynamic type determination for VCF files Mark DePristo 2011-08-08 14:45:46 -0400
  • 9756c1d7d7 Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-08 14:16:31 -0400
  • 221b71c5a4 add 2nd round of counting covariates Eric Banks 2011-08-08 14:16:16 -0400
  • e36994e36b Refactored a FeatureManager class from RMDTrackBuilder Mark DePristo 2011-08-08 14:04:46 -0400
  • 197169e47b Submitting patch from Larry Singh to make MathUtils compatible with java 1.7 Eric Banks 2011-08-08 13:34:04 -0400
  • dd974040af When finding the highest-impact effect at a locus, all effects that are not within a non-coding gene are now considered higher impact than all effects that are within a non-coding gene. David Roazen 2011-08-08 10:46:18 -0400
  • c1061e994c Initial support for adding genomic annotations through VariantAnnotator using the output from the SnpEff tool, which replaces the old Genomic Annotator. David Roazen 2011-08-04 19:36:26 -0400
  • 1a0e5ab4ba Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-08 13:08:25 -0400
  • a06f341685 qscript to assess BQSR known sets Eric Banks 2011-08-08 13:08:17 -0400
  • 99e3a72343 Merged bug fix from Stable into Unstable Ryan Poplin 2011-08-08 12:36:17 -0400
  • 8072bd9831 Updating resource bundle generation qscript for changeover to git Ryan Poplin 2011-08-08 12:35:39 -0400
  • 0db79207e8 Refactored dependancy from CommandLineGATK from javadocs Mark DePristo 2011-08-08 12:27:13 -0400
  • 0db46d0648 Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-08-08 10:50:09 -0400
  • 2fd101135c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Mauricio Carneiro 2011-08-08 10:49:43 -0400
  • 4d6cb33612 removing temporary bam index Mauricio Carneiro 2011-08-08 10:49:28 -0400
  • e5fde0d16b Merge branch 'master' into rodRefactor Mark DePristo 2011-08-08 10:08:43 -0400
  • 88061ed5fa rmdir the empty tmp dir if possible Mark DePristo 2011-08-08 09:18:20 -0400
  • 526b524c3c CombineVariants with new RodBinding. Bugfix Mark DePristo 2011-08-07 20:16:51 -0400
  • 6693407bd8 Merged bug fix from Stable into Unstable Ryan Poplin 2011-08-07 17:39:03 -0400
  • 738e94efcb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Ryan Poplin 2011-08-07 17:36:45 -0400
  • b3e57c329a Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-07 15:18:15 -0400
  • 5f8bc3aa8a Documenting classes, and name cleanup Mark DePristo 2011-08-07 15:17:50 -0400
  • 1c63d43176 Help now points to GATKDocs instead of spitting out full, garbled description Mark DePristo 2011-08-07 15:02:46 -0400
  • 1d8b1bae0a Need to rename the integration test argument -mask to -maskName Mark DePristo 2011-08-07 13:32:26 -0400
  • 3c7a96cf2d Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-07 12:12:47 -0400
  • be0fc8a1e0 Now creates .gz archive of s3 downloads Mark DePristo 2011-08-07 12:11:50 -0400
  • ece8f0db5e Added b37dbSNP129, needed for Queue Mark DePristo 2011-08-07 11:26:07 -0400
  • b0e91f85cf fix merge from Khalid's Queue fix Mark DePristo 2011-08-07 10:33:20 -0400
  • 4d88e72958 Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor Mark DePristo 2011-08-07 10:32:27 -0400
  • f049461120 Changed @Argument to @Input on input RodBindings. Changed shortname collision with longname. Restored scala builds. Updated HSP to use new syntax. Khalid Shakir 2011-08-06 20:44:19 -0400
  • f534c2e7bb Merged bug fix from Stable into Unstable Khalid Shakir 2011-08-06 10:43:52 -0400
  • eaa2f16d83 When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED. Khalid Shakir 2011-08-06 10:42:04 -0400
  • 573700d18d Adding missing import Mark DePristo 2011-08-04 21:57:00 -0400
  • 14e43c3382 Final fix to RodBindingUnitTest to reset global counter variable Mark DePristo 2011-08-04 21:52:39 -0400
  • d7f98e5c2a Fixed merge conflict deleting a { Mark DePristo 2011-08-04 18:48:34 -0400
  • 75632abf88 Merge branch 'master' into rodRefactor Mark DePristo 2011-08-04 18:44:14 -0400
  • f21f7f6335 SelectVariants fully documented, now the shining example of the new RodBinding system. Mark DePristo 2011-08-04 18:28:59 -0400
  • 9308fbe3fb VariantEval Integration Test parameterized for new novelty stratification Mark DePristo 2011-08-04 18:08:47 -0400
  • 9be1ee59cc TODO comments for Eric Mark DePristo 2011-08-04 18:07:50 -0400
  • b22a3d6508 Functional VCF output. Mauricio Carneiro 2011-08-04 17:49:08 -0400
  • a8eb8c27f0 a) Minor changes to indel consensus scripts to better reflect good default values, b) Fixed up Mills/Devine codec so it always produces correct ref padded bases, and added option to VariantsToVCF to fix reference base Guillermo del Angel 2011-08-04 15:34:49 -0400
  • 98a96f07c1 Updated standard deviation parameter in VQSR to our current recommended value Ryan Poplin 2011-08-04 14:06:26 -0400
  • 406982284c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-04 12:49:02 -0400
  • 58a60d4901 Merge branch 'master' into rodRefactor Mark DePristo 2011-08-04 12:48:56 -0400
  • e48492f3c3 Validate that the reference padding base for indels is correct. Eric Banks 2011-08-04 12:48:56 -0400
  • d2078f09b2 Minor fixes to ITs Mark DePristo 2011-08-04 12:47:55 -0400
  • f10588420c Fixing path to dbSNP file as the other one was replaced Eric Banks 2011-08-04 12:36:24 -0400
  • 21dc9a5543 Adding mills/devine indel dataset to the resource bundle Ryan Poplin 2011-08-04 12:31:28 -0400
  • f0d798d47c Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once. Mark DePristo 2011-08-04 12:06:10 -0400
  • 0739b7f75b Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-08-04 11:07:25 -0400
  • aff681e407 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Mauricio Carneiro 2011-08-04 11:05:25 -0400
  • fa97bd8ac1 Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-08-04 09:52:10 -0400
  • 23ec5b94cf fixed a missing check for null Mauricio Carneiro 2011-08-04 09:50:02 -0400
  • 490ca475fc Replacing hardcoded dbsnp129 with BaseTest variable Mark DePristo 2011-08-03 22:15:22 -0400
  • a831af1166 Another misprint when removing the references to -D Eric Banks 2011-08-03 21:29:21 -0400
  • d0279bb28c RodBinding names are now defaulting to the ArgumentTypeDescriptor fullname Mark DePristo 2011-08-03 20:48:11 -0400
  • d8f1ebf8c6 Parameterized RecalibrationWalkers with clean unstable database Mark DePristo 2011-08-03 20:06:00 -0400
  • 41b3840d26 Took latest VEIT and updated to use dbsnp132 vcf Mark DePristo 2011-08-03 18:40:32 -0400
  • 0ef85647f7 A working version of a GATKReportDiffableReader for the diffEngine! Mark DePristo 2011-08-03 18:21:18 -0400
  • b68ed62632 Clean now removes gatkdocs Mark DePristo 2011-08-03 18:11:22 -0400
  • acbd3d0922 Fixing up integration tests so more Mark DePristo 2011-08-03 17:26:35 -0400
  • 8f696c7731 Continuing progress towards RodBinding 1.0 Mark DePristo 2011-08-03 17:19:28 -0400
  • 800bb97f0b Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser Mark DePristo 2011-08-03 16:04:51 -0400
  • 8981367307 Updating memory usage for picard programs Mauricio Carneiro 2011-08-03 15:48:28 -0400
  • f6563c0f9f Removed support for RMD in @Requires and @Allows Mark DePristo 2011-08-03 15:36:55 -0400
  • 79e4a8f6d3 Merge Mark DePristo 2011-08-03 15:09:47 -0400
  • 38efd3066c Bug fix for mask RodBinding Mark DePristo 2011-08-03 14:58:18 -0400
  • f62f47d476 Not sure why this didn't fail before, but bringing VE up to date with previous changes Eric Banks 2011-08-03 14:27:07 -0400
  • b25140db83 Contracts and documentation for some of RefMetaDataTracker Mark DePristo 2011-08-03 13:34:20 -0400
  • 3de10b1ef8 Fixing misprint from Ryan's commit Eric Banks 2011-08-03 12:37:50 -0400
  • db2e0aaa1a Darn, forgot to update unit tests. Eric Banks 2011-08-03 12:31:08 -0400
  • 020b2408a8 Adding integration test for left alignment of indels Eric Banks 2011-08-03 12:19:44 -0400
  • f6648e0144 Don't left-align complex indels because it's too complicated. Eric Banks 2011-08-03 12:03:50 -0400
  • 85c67e9891 Contracts and documentation for Rodbinding Mark DePristo 2011-08-03 11:16:06 -0400
  • 5dc324ff35 Dealing with merge confict Eric Banks 2011-08-03 11:03:47 -0400
  • 7c89fe01b3 Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record. Eric Banks 2011-08-03 11:00:36 -0400
  • d9bc673ff2 Fixed bad constructor in RMDTUnitTest Mark DePristo 2011-08-03 09:42:43 -0400
  • 3e043a633c Merged bug fix from Stable into Unstable Khalid Shakir 2011-08-03 02:23:16 -0400
  • a587f38808 Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf". Khalid Shakir 2011-08-03 02:21:01 -0400
  • 5dcac7b064 GATKReport v0.2: - Floating point column widths are measured correctly - Using fixed width columns instead of white space separated which allows spaces embedded in cell values - Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width - Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly Replaced GATKReportTableParser with existing functionality in GATKReport Khalid Shakir 2011-08-03 00:24:47 -0400
  • 2874835997 Bug fix for type checking RodBindings Mark DePristo 2011-08-02 22:25:41 -0400
  • b5e843f8f0 Approaching the end for the new RodBinding system Mark DePristo 2011-08-02 22:00:06 -0400
  • d3437e62da Added a simple utility method Utils.optimumHashSize() to calculate the optimum initial size for a Java hash table (HashMap, HashSet, etc.) given an expected maximum number of elements. The optimum size is the smallest size that's guaranteed not to result in any rehash / table-resize operations. David Roazen 2011-08-02 21:59:06 -0400
  • 83891271b5 --variants throughout integrationtests Mark DePristo 2011-08-02 20:28:47 -0400
  • 3a27a25cfc Validates that the tribble binding provides the right object types at startup Mark DePristo 2011-08-02 20:11:24 -0400
  • df37716857 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-02 18:27:13 -0400
  • daeabe6a2f Updated HybridSelectionPipelineTest's variant count and titv to match expectations based on ebanks removing strand bias. TODO: update filtering/recalibrations in HSP. Khalid Shakir 2011-08-02 17:09:16 -0400
  • 20afe2a437 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-02 15:34:52 -0400
  • b2cde87378 Removing --DBSNP syntax from BQSR integration tests Ryan Poplin 2011-08-02 15:34:38 -0400
  • c2dc7c9c99 Updated flanks eval the same way the targets eval was updated by ebanks. Khalid Shakir 2011-08-02 15:30:04 -0400
  • e4a67f3df1 RefMetaDataTracker has complete set of get() functions for List<RodBinding<T>> Mark DePristo 2011-08-02 14:28:35 -0400
  • 03741fb640 Merge branch 'master' into rodRefactor Mark DePristo 2011-08-02 14:21:58 -0400
  • a366f9a18d Updating tools to use the RodBinding<T> syntax Mark DePristo 2011-08-02 14:05:51 -0400