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• 43bd6b4436 Merge pull request #689 from broadinstitute/eb_fix_samrecord_test_constructor Eric Banks 2014-07-23 23:03:30 -0400
• 84af1fc75f The copy constructor for a GATKSAMRecord (used for testing only) should use the actual read's contig index, not its mate's. Eric Banks 2014-07-23 15:31:03 -0400
• 881fc9cc35 Merge pull request #687 from broadinstitute/vrr_omniploidy_assesment_na12878 Valentin Ruano Rubio 2014-07-22 14:45:59 -0400
• a3d180ac43 Updated na12878kb-utils with classes from old ant StingUtils.jar. Fixed package names post picard/htsjdk renaming. Khalid Shakir 2014-07-22 23:31:47 +0800
• 8c14609477 Added -gtType argument to AssessNA12878 to stratify assessment based on true genotype call in NA12878 (or input call if the former is not in KB). Valentin Ruano-Rubio 2014-07-15 15:46:34 -0400
• 0798a4b768 Update pom versions to mark the start of GATK 3.3 development David Roazen 2014-07-17 12:09:33 -0400
• 323f22f852 Update pom versions for the 3.2 release David Roazen 2014-07-17 12:06:22 -0400
• 98d88eb07e Fixed IndexOutOfBounds error associated with tail merging. Eric Banks 2014-07-16 23:14:33 -0400
• 799071b520 Merge remote-tracking branch 'unstable/master' David Roazen 2014-07-14 14:07:16 -0400
• 104d94a1ac Merge pull request #686 from broadinstitute/gg_gatkdocs_updates Geraldine Van der Auwera 2014-07-14 12:10:36 -0400
• a6f632874b Various documentation improvements Geraldine Van der Auwera 2014-05-21 12:35:22 -0400
• db53d096c9 Merge pull request #684 from broadinstitute/ks_add_cofoja_to_gatk_packages droazen 2014-07-14 11:15:49 -0400
• 2138aa135c Merge pull request #683 from broadinstitute/eb_disable_complex_variant_merging_PT74816146 Eric Banks 2014-07-13 08:57:13 -0400
• ecefcb383d Disable the complex variant merging for now, as requested by ATGU Eric Banks 2014-07-11 15:08:43 -0400
• c7e357eb59 Added cofoja to the gatk packages for tests to pass. Khalid Shakir 2014-07-11 23:19:42 +0800
• b8751ad598 Merge pull request #680 from broadinstitute/ldg_VQSRscript droazen 2014-07-11 10:16:37 -0400
• 4f4ff5c327 Merge pull request #682 from broadinstitute/ks_revert_md5_db_per_test kshakir 2014-07-11 03:42:18 +0800
• 193e389b41 Merge pull request #679 from broadinstitute/eb_better_tail_merging_PT74222522 Ryan Poplin 2014-07-10 13:54:33 -0400
• 598b481733 Merge pull request #671 from broadinstitute/vrr_omniploidy_assesment_na12878 Valentin Ruano Rubio 2014-07-10 13:19:32 -0400
• 18f6d56b4c Revert "Using the base directory for each test run when outputting MD5DB mismatches." Khalid Shakir 2014-07-11 01:11:25 +0800
• cc09ef9190 Revert "Appending to md5db in the gatkdir, with additional logging." Khalid Shakir 2014-07-11 01:11:20 +0800
• a105cc4c0a Merge pull request #681 from broadinstitute/dr_md5mismatch_generator_script droazen 2014-07-10 10:40:09 -0400
• af0aab8791 Shell script to generate md5 mismatches file from a Bamboo log of an integration test run David Roazen 2014-07-10 10:32:10 -0400
• 1d97b4a191 Improved tail merging: now tails can be merged to branches that are not entirely reference. Eric Banks 2014-07-02 14:59:18 -0400
• aecd34d274 Merge pull request #677 from broadinstitute/ks_md5_db_per_test_type kshakir 2014-07-10 17:53:24 +0800
• 5eee065133 Merge pull request #674 from broadinstitute/rp_improve_genotyping Ryan Poplin 2014-07-09 16:03:09 -0400
• a7d1904c63 Appending to md5db in the gatkdir, with additional logging. Khalid Shakir 2014-07-09 23:12:56 +0800
• 99026eb51b Update VQSR Rnd BQSR script generation code for compatibility with latest ggplot version. Update queueJobReport.R and public/gsalib/src/R/R/gsa.variantqc.utils.R also Laura Gauthier 2014-07-08 11:14:07 -0400
• cd2c5ce1b2 Now AssessNA12878 can handle different input ploidy for omniploidy assessment where we may run HC as if it was a haploid, tetraploid (and so forth) organism. Valentin Ruano-Rubio 2014-07-02 15:30:13 -0400
• a85bc0b577 Merge pull request #678 from broadinstitute/dr_remove_junit_imports droazen 2014-07-09 14:40:38 -0400
• 74a7674d70 Improvements to genotyping accuracy. Ryan Poplin 2014-07-08 11:07:19 -0400
• 719e685759 Remove junit imports in the test suite David Roazen 2014-07-09 12:09:27 -0400
• 465c5ed9b0 Merge pull request #676 from broadinstitute/cww_junit_assert droazen 2014-07-08 16:12:34 -0400
• 635b9bd1af Replace improper use of org.junit imports with org.testng. Chris Whelan 2014-07-08 16:07:39 -0400
• b2e51838d7 Merge pull request #673 from broadinstitute/ks_md5_db_per_test_run droazen 2014-07-08 10:58:59 -0400
• 2129aa05d8 Bug fix for poms missing package test artifacts. Khalid Shakir 2014-07-08 06:29:47 +0800
• e5be9c7073 Using the base directory for each test run when outputting MD5DB mismatches. Khalid Shakir 2014-07-08 06:28:16 +0800
• f084fa5ab2 Merge pull request #669 from broadinstitute/eb_improve_decomposition_of_haplotypes_PT71966916 Ryan Poplin 2014-07-02 10:08:32 -0400
• bad7865078 When converting a haplotype to a set of variants we now check for cases that are overly complex. Eric Banks 2014-07-01 10:19:10 -0400
• 297c2b0651 Merge pull request #670 from broadinstitute/rp_SBBS_min_count ldgauthier 2014-07-01 08:34:23 -0400
• e14bff212d SB tables should be created even if the ref or alt columns have no counts. This is so that FS/SOR will still be calculated when the variant is extremely high or low frequency. Ryan Poplin 2014-06-25 13:36:26 -0400
• 5c45641051 Merge pull request #668 from broadinstitute/rp_AD_realigned_reads_8b9d1c1 Ryan Poplin 2014-06-30 12:35:40 -0400
• 0127799cba Reads are now realigned to the most likely haplotype before being used by the annotations. Ryan Poplin 2014-06-11 15:45:45 -0400
• dc93507023 Merge pull request #667 from broadinstitute/ks_refactor_doc_scala_package jmthibault79 2014-06-25 16:05:30 -0400
• f5345e903a Fixed minor pom.xml line that was out of place after sortpom. Khalid Shakir 2014-06-26 01:00:35 +0800
• 7b5f88a49c Refactored DoC custom Queue wrappers to a non-package object. Now, "mvn verify && mvn verify" should work again. Khalid Shakir 2014-06-26 00:59:18 +0800
• b935ed0df1 Merge pull request #665 from broadinstitute/ks_force_delete_bad_symlinks droazen 2014-06-25 00:13:05 -0400
• 92028027c9 Merge pull request #666 from broadinstitute/pd_merge_selectvariants_test Eric Banks 2014-06-24 21:19:46 -0400
• 06d619e9aa Removed redundant SelectVariantsIntegrationTest, merged it's only test into protected version Phillip Dexheimer 2014-06-24 18:59:59 -0400
• 45d819a00e For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. Better than running it during the "clean" phase, since these users may not run "mvn clean" before attempting to build. Khalid Shakir 2014-06-25 02:32:15 +0800
• 42cfa3b53b Merge pull request #664 from broadinstitute/ks_picard_maven_gatk_root kshakir 2014-06-24 18:48:40 +0800
• bffc9fbabd Fixed gatk-root path in private/picard-maven/pom.xml Khalid Shakir 2014-06-24 18:45:51 +0800
• c191103326 Merge pull request #663 from broadinstitute/pd_jexl_user_exception Eric Banks 2014-06-20 17:17:54 -0400
• 65eeb4a7ab Recast the "Invalid JEXL expression detected" error in SelectVariants from a RuntimeException to a UserException - PT 68931448 Phillip Dexheimer 2014-06-19 23:52:26 -0400
• db7dc8ab5f Merge pull request #660 from broadinstitute/pd_catvariants_list Eric Banks 2014-06-19 23:54:03 -0400
• da5e567b73 Added functionality to CatVariants to process .list files with -V - Pivotal 70305712 Phillip Dexheimer 2014-06-17 23:38:03 -0400
• da1dab6c32 Merge pull request #661 from broadinstitute/jw_allele_balance_gvcf Ryan Poplin 2014-06-19 13:10:41 -0400
• 41d2a793f0 Merge pull request #662 from broadinstitute/eb_Carlos_Borroto_commits Eric Banks 2014-06-19 12:49:14 -0400
• 1092dd6e25 From Carlos Barroto: switch outputRoot in SplitSamFile to an empty string instead of null. Eric Banks 2014-06-19 10:05:51 -0400
• 9212edba41 From Carlos Barroto: made 'level' in Picard's CalculateHsMetrics Scala Queue extension an argument. Eric Banks 2014-06-19 10:04:04 -0400
• 8b75428a90 Enable AB annotation in reference model pipeline. Incorporates patches from John Wallace to public github account Ryan Poplin 2014-06-19 09:35:04 -0400
• 2df2a153e6 Merge pull request #658 from broadinstitute/ldg_PbyTwithPriors Eric Banks 2014-06-18 15:04:39 -0400
• 9640d5d745 Merge pull request #649 from broadinstitute/pd_genotypegvcf_args Eric Banks 2014-06-18 11:36:13 -0400
• 2356d5d63f Updated CalculateGenotypePosteriors to compute genotype posteriors using likelihoods from all members of the trio. (Right now it only works if all members of the trio are called.) Takes posteriors as input, defaulting to PLs Added annotations for possible de novos for us in full genotype refinement pipeline Added family priors to CGP integration test. Changed CGP to use PP tag instead of GP tag because posteriors are Phred-scaled. Updated CGP integration test md5s to reflect change. Laura Gauthier 2014-04-30 13:55:28 -0400
• 7570666f2a Merge pull request #655 from broadinstitute/nfd_mathutil_opts Nigel Delaney 2014-06-17 17:07:42 -0400
• 5e258bfeff Minor optimization to function to calculate the log of exponentials. Nigel Delaney 2014-06-11 16:18:32 -0400
• 0ce28b78e0 Merge pull request #657 from broadinstitute/rp_ref_model_pipeline_noMQ_indels Ryan Poplin 2014-06-16 11:29:11 -0400
• 9390c56d52 Using MQRanksum for indels was a bad idea according to the knowledgebase. Removing from the ref model pipeline. Indels create mapping quality biases that aren't indicitive of error. Ryan Poplin 2014-06-16 11:28:33 -0400
• 2e78815055 Added missing arguments to GenotypeGVCFs - New arguments are nda, hets, indelHeterozygosity, stand_call_conf, stand_emit_conf, ploidy, and maxAltAlleles - Addresses PT 70110918 - To do this, moved those arguments out of the StandardCallerArgumentCollection into a new GenotypeCalculationArgumentCollection, which is now included as a member of SCAC Phillip Dexheimer 2014-05-28 22:11:56 -0400
• 838304cc89 Merge pull request #656 from broadinstitute/cww_fastSiblingIBD Eric Banks 2014-06-13 11:37:31 -0400
• 01380d20a5 Added licenses to siblingibd classes Chris Whelan 2014-06-13 10:09:33 -0400
• 164d270447 Merge pull request #651 from broadinstitute/cww_fastSiblingIBD Eric Banks 2014-06-13 09:51:33 -0400
• ba1d23e535 Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings. -When parental genotypes are available, implements an HMM on genotype observations in the quartet. -Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state. -Includes an experimental heuristic based mode for when parental genotypes are not available. -Made a method in MendelianViolation public static to reuse code. -Added the mockito library to private/gatk-tools-private/pom.xml Chris Whelan 2014-05-07 10:10:52 -0400
• fbc75c8e14 Merge pull request #654 from broadinstitute/rp_gvcf_indexing_strategy Ryan Poplin 2014-06-12 10:45:25 -0400
• b61b16ac6d Adding the required GVCF indexing strategy arguments. Ryan Poplin 2014-06-12 10:41:36 -0400
• 5493126034 Merge pull request #653 from broadinstitute/rp_updated_ref_model_qscript Ryan Poplin 2014-06-12 09:52:17 -0400
• 58e9e7df95 Updating the ref model pipeline qscript. Ryan Poplin 2014-06-12 09:51:33 -0400
• 3079755b4c Merge pull request #646 from broadinstitute/ks_disable_distribution_with_private droazen 2014-06-11 11:00:31 -0400
• f082572593 If passed -Pgsadev, don't build the distribution package. Khalid Shakir 2014-05-28 12:41:55 -0400
• a20da6b9aa Merge pull request #650 from broadinstitute/xhmm_Qscript Eric Banks 2014-06-10 10:20:21 -0400
• a1868e8b82 For XHMM and Depth-of-Coverage Qscripts, add ability for user to input sample renaming file at the GATK level using existing GATK flag (--sample_rename_mapping_file) and custom pre-processing code. For XHMM Qscript, add scatter-gather for Discovery and Genotype stages. Menachem Fromer 2014-06-09 23:49:54 -0400
• ea98a59c78 Stop downloading GATK reports from legacy AWS account David Roazen 2014-06-06 15:19:28 -0400
• 4ea53f7132 Merge pull request #647 from broadinstitute/pd_output_dir_check jmthibault79 2014-06-03 10:07:24 -0400
• 4eb9858461 Ensure that output files are specified in a writeable location -PT 69579780 Phillip Dexheimer 2014-05-28 22:44:37 -0400
• db96891d4b Merge pull request #638 from broadinstitute/vrr_createTempFile_testfix Valentin Ruano Rubio 2014-05-29 10:15:05 -0400
• 07567fdae3 Removed debug code outputing files not removed after VM exists in ReadThreadingLikelihoodCalculationEngineUnitTest. Notice however that this should not be the cause of resent problems as the code was desactivated. Valentin Ruano-Rubio 2014-05-28 19:03:25 -0400
• 938172d7f0 Removed redundant overrride createTempFileFromBase (same code as super class) and added some finals to DepthOfCoverageB36IntegrationTest Valentin Ruano-Rubio 2014-05-28 19:02:04 -0400
• e0c221470c Changed File.createTempFile to BaseTest.createTempFile Valentin Ruano-Rubio 2014-05-28 18:59:48 -0400
• ef7531d4a5 Merge pull request #640 from broadinstitute/IntegerSWImplementation EvolvedMicrobe 2014-05-28 15:10:05 -0400
• cc45e62e8e Change SmithWaterman to use integers instead of doubles. Nigel Delaney 2014-05-25 17:12:00 -0400
• ac52fa581a Merge pull request #644 from broadinstitute/ks_queue_test_temp_fix droazen 2014-05-28 11:29:08 -0400
• ff43b1f298 Merge pull request #636 from broadinstitute/pd_log10_refactor Eric Banks 2014-05-28 08:46:49 -0400
• ed66f690dd Merge pull request #645 from broadinstitute/pd_progress_format Eric Banks 2014-05-28 08:45:26 -0400
• 6122b2805d Legibility improvements to ProgressMeter - Fields in the header are delimited with the pipe character - Header is now split into two lines to improve spacing - Field width in header and progress lines auto-adjusts to length of "processing units" label (sites, active regions, etc) - Addresses PT 69725930 Phillip Dexheimer 2014-05-27 23:52:42 -0400
• c15e6fcc0e Refactored the static lookup arrays in MathUtils (log10Cache, log10FactorialCache, jacobianLogTable) -They are now only computed when necessary -Log10Cache is dynamically resizable, either by calling get() on an out-of-range value or by calling ensureCacheContains -Log10FactorialCache and JacobianLogTable are initialized to a fixed size on first access and are not resizable -Addresses PT 69124396 Phillip Dexheimer 2014-05-18 20:26:24 -0400
• b77589696e Merge pull request #643 from broadinstitute/rp_remove_hwp Eric Banks 2014-05-27 17:21:19 -0400
• 6c9e68ef41 Disabled ExampleUG Queue Tests, fixed internal extensions dependency. EUG tests disabled due to new protected qscript directory path, post GATK artifact splitting. Khalid Shakir 2014-05-27 16:16:53 -0400
• 3f694d61ee Merge pull request #641 from broadinstitute/dr_post_test_cleanup Eric Banks 2014-05-27 15:59:03 -0400
• 400d19a126 Merge pull request #642 from broadinstitute/dr_maven_symlink_cleanup_script Eric Banks 2014-05-27 15:52:18 -0400
• 6ca483e574 Script to manually delete maven-created symlinks to testdata/qscripts David Roazen 2014-05-27 15:33:11 -0400