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  • 61e1a3ecd1 Added the framework for testing the PhasingUtilies methods matchHaplotypeAlleles() and reallyMergeIntoMNP() Ron Levine 2014-11-22 22:01:39 -0500
  • ba5a32107f Merge pull request #778 from broadinstitute/mf_RBP_MNP_merging rpoplin 2014-11-21 16:00:42 -0500
  • 9b73c8a841 Fix MNP merging bugs Menachem Fromer 2014-11-21 06:42:51 -0500
  • 00027e1555 Merge pull request #774 from broadinstitute/ldg_makeSelectVariantsTrimAlleles rpoplin 2014-11-13 13:58:13 -0500
  • bcac930aad Merge pull request #773 from broadinstitute/rhl_annotator_warning ldgauthier 2014-11-12 08:01:19 -0500
  • 67656bab23 Resolved conflict during rebasing Ron Levine 2014-11-04 18:15:49 -0500
  • 783a4fd651 Change default behavior of SelectVariants to trim remaining alleles when samples are subset. -noTrim argument preserves original alleles. Add test for trimming. Laura Gauthier 2014-11-07 10:28:53 -0500
  • dc0cd7625a Merge pull request #775 from broadinstitute/vrr_hc_bamout_wrong_indel_start rpoplin 2014-11-10 15:10:16 -0500
  • c5977e5c8f Correct wrong left-alignment of reads in HC bamout Valentin Ruano-Rubio 2014-11-06 18:03:52 -0500
  • 31cb47b9e6 Merge pull request #763 from broadinstitute/ldg_combineGVCFsFix rpoplin 2014-11-06 12:56:15 -0500
  • 8ddcff159e Merge pull request #765 from broadinstitute/rhl_improve_bad_file_err_msg jmthibault79 2014-11-05 10:59:38 -0500
  • 6f78bf5041 Catch RuntimeException and add the bad file name to the newly thown exception Ron Levine 2014-10-28 10:31:39 -0400
  • c09667a20d Fix bug in CombineGVCFs so now sample 2 variants occuring within sample 1 deletions get merged properly. CombineGVCFs now outputs ref conf for the duration of deletions so that SNPs occuring in other samples aligned with those deletions will be genotyped correctly Laura Gauthier 2014-10-22 15:29:13 -0400
  • c14fccb571 Merge pull request #771 from broadinstitute/ks_faster_builds kshakir 2014-11-05 01:54:59 +0800
  • 0092a0b9eb Faster builds, with updates to documentation generation. Reading the multiple GATKText files as a single stream, especially with new top level target executable jar files pointing to a lib folder. Don't dirty the build with a new GATKText.properties if input files are unmodified. Stop warning on undocumented abstract classes. Fixed ClassNotFoundException/NoClassDefFoundError by fixing ResourceBundleExtractorDoclet artifact. Excluding Exceptions from documentation. Removed custom log4j dependency from ResourceBundleExtractorDoclet. Stop generating the dependency reduced pom during shade. Stop regenerating gsalib when the files are already up to date. Disabled mvn site generation from external-example. Khalid Shakir 2014-11-02 16:18:23 +0900
  • 1cb4b99548 Added faster built executable, non-packaged jars. Moved top level target symlinks to package jar files to under target/package. Executable jar files are placed under target/executable with the new target[/lib] directories. Under top level target, symlinks to *either* the package *or* the executable jars replace what was a symlink to the package jar path. Allow disabling of the shade package. ant-bridge.sh by default only builds executable jars, and doesn't package by default, as did the old ant build.xml. Added a new package_path.sh utility script for other scripts to use instead of anything in the target folder. Khalid Shakir 2014-11-02 16:18:07 +0900
  • f6af776590 Merge pull request #767 from broadinstitute/gg_fix_gsalib_doc rpoplin 2014-11-04 10:46:27 -0500
  • 65d834fece Merge pull request #769 from broadinstitute/pd_sb_plusplus rpoplin 2014-11-04 10:45:46 -0500
  • 10f99cbe04 Added StrandAlleleCountsBySample annotation Phillip Dexheimer 2014-10-29 22:27:18 -0400
  • 20bab93634 Merge pull request #772 from broadinstitute/ks_disable_lsf_tests droazen 2014-11-03 16:24:57 -0500
  • 8b81031bf8 Disabling tests for Lsf706 specific functionality. Khalid Shakir 2014-11-03 22:10:39 +0800
  • f93b5b2c39 Merge pull request #770 from broadinstitute/pd_ngs_platform rpoplin 2014-11-03 10:15:17 -0500
  • bcfd9ce19a Moved platform flow information into NGSPlatform * Explicitly added a type for rarely used platforms * PT 81767718 Phillip Dexheimer 2014-10-31 22:27:34 -0400
  • c84805c402 Merge pull request #768 from broadinstitute/pd_bcf_failures rpoplin 2014-10-31 15:30:56 -0400
  • eecb56e0ae Merge pull request #766 from broadinstitute/ldg_StrandBiasForMultiallelics rpoplin 2014-10-31 15:26:07 -0400
  • 2ff88d17ca Merge pull request #764 from broadinstitute/ldg_fixCombineVariantsError rpoplin 2014-10-31 15:23:23 -0400
  • 2d7f906a27 Merge pull request #762 from broadinstitute/ks_refactor_mvn_packages kshakir 2014-11-01 02:17:01 +0900
  • fc67e50faa Revved Picard/htsjdk Removed inefficient array->List conversion in AlleleCountBySample Phillip Dexheimer 2014-10-29 20:32:05 -0400
  • b3b569f43a Picard made major changes post-v1.123. Update our tools to handle them Phillip Dexheimer 2014-10-23 21:42:05 -0400
  • e351ca869d Updated gsalib package to match version we put in CRAN Geraldine Van der Auwera 2014-10-30 14:26:38 -0400
  • bc7202fff7 Calculate StrandBiasBySample using all alternate alleles as ref vs. any alt Laura Gauthier 2014-08-20 10:27:27 -0400
  • 4d3db58c71 Added a compile time script to enforce utils/engine/tools separation. Khalid Shakir 2014-10-22 00:40:47 +0800
  • 7bae70ec1a Minor change to new CombineVariants error check so identical samples don't need genotypeMergeOption Laura Gauthier 2014-10-28 08:17:49 -0400
  • 5c9fe1a06d Split all imports of tools|engine from utils, and all tools from engine. Second of two commits, modifying actual files. Khalid Shakir 2014-10-22 00:40:45 +0800
  • bb7151192a Split all imports of tools|engine from utils, and all tools from engine. First of two commits, renaming files only. Khalid Shakir 2014-10-22 00:40:42 +0800
  • b69b256003 Update pom versions to mark the start of GATK 3.4 development Geraldine Van der Auwera 2014-10-23 22:31:44 -0400
  • eee94ec81f Update pom versions for the 3.3 release Geraldine Van der Auwera 2014-10-23 22:25:17 -0400
  • a5aa4d5822 Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2014-10-23 22:23:22 -0400
  • 22230cc820 Merge pull request #761 from broadinstitute/ks_junction_plugin_local_repo Geraldine Van der Auwera 2014-10-23 19:12:41 -0400
  • 75c17bbd6f Adding sysinternals:junction:1.04:exe to local repo. With Geraldine's blessing, works around issue where the repo for this exe keeps going down. Khalid Shakir 2014-10-24 05:29:31 +0800
  • 37464c38f2 Merge pull request #760 from broadinstitute/ks_queue_patches droazen 2014-10-23 14:52:26 -0400
  • ac33eda231 Queue patches. Fixed Queue bug with bad localhost addresses. Spaces in job names, while fine in GridEngine 6, break in (Son of) GE8. Khalid Shakir 2014-10-23 22:59:19 +0800
  • 7dc8638ca4 Merge pull request #759 from broadinstitute/gg_minor_docfixes Geraldine Van der Auwera 2014-10-22 22:20:26 -0400
  • 3ba94b987c Minor documentation clarifications Geraldine Van der Auwera 2014-10-22 17:54:11 -0400
  • 0f89d1a362 Merge pull request #755 from broadinstitute/sc_Annotation_Docs_73647570 rpoplin 2014-10-22 13:41:00 -0400
  • f093950bf9 Merge pull request #740 from broadinstitute/rp_ROC_curve_total_sensitivity rpoplin 2014-10-22 11:33:16 -0400
  • e2fec7582e Merge pull request #756 from broadinstitute/gg_fixGenotypeAndValidate rpoplin 2014-10-22 09:43:42 -0400
  • be4cbf7035 Merge pull request #757 from broadinstitute/ks_smowton_scatter_contigs_fix kshakir 2014-10-22 19:27:02 +0800
  • 26ba4c11aa Minor fixups for previous commit once tests (only runnable at Broad) were run. Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals(). In test for fewer files than intervals, adjusted expected intervals. In test for more files than intervals, adjusted expected exception. Khalid Shakir 2014-10-22 17:37:37 +0800
  • a62dc84795 Improved scatter contigs algorithm to be fairer when splitting a large number of contigs into a small number of parts. Chris Smowton 2014-10-07 15:35:45 +0100
  • b3c5ed4414 Improvements to documentation of variant annotations Sheila Chandran 2014-07-24 12:45:19 -0400
  • 895b8c5931 Minor fix for missing INFO key definition in VCF header Geraldine Van der Auwera 2014-10-21 15:21:12 -0400
  • edaa78dea1 Merge pull request #743 from broadinstitute/gg_gsaweb_switchover droazen 2014-10-21 12:27:51 -0400
  • c4fcd70a88 Merge pull request #754 from broadinstitute/rhl_variant_array_exception rpoplin 2014-10-21 12:01:52 -0400
  • bcf6be0b08 Merge pull request #753 from broadinstitute/ldg_HCzeroDepth rpoplin 2014-10-21 12:00:04 -0400
  • 7ec38bf2a2 Merge pull request #752 from broadinstitute/pd_cran_license rpoplin 2014-10-21 11:51:24 -0400
  • 312a833db3 Merge pull request #751 from broadinstitute/pd_bamout_ref_regions rpoplin 2014-10-21 11:50:46 -0400
  • 2b848ad859 Variants that become hom-ref after regenotyping in GenotypeGVCFs are now getting output in -allSites mode. Laura Gauthier 2014-10-17 10:28:15 -0400
  • 5465e4484e For GenotypeGVCFs -allSites mode, make genotypes no-call if depth is zero. Laura Gauthier 2014-10-17 09:26:38 -0400
  • 239151ac7b Do not process a variant if it is too large (> readLength), and log an error Ron Levine 2014-10-14 17:08:48 -0400
  • f766608b4e Changed license of gsalib R package from BSD to MIT - PT 75827540 Phillip Dexheimer 2014-10-16 21:37:07 -0400
  • b348ce8f25 Added -disableOptimizations argument to HaplotypeCaller. * This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam * Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter * Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case * Addresses PT 77731660 Phillip Dexheimer 2014-09-10 22:16:12 -0400
  • 5fa5724e4a Merge pull request #750 from broadinstitute/ldg_uniqueSamplesInCombineVariants ldgauthier 2014-10-16 07:57:27 -0400
  • 0f08065ebc Throw UserException if input VCFs have duplicate samples but no genotypemergeoption is specified Laura Gauthier 2014-10-15 12:41:45 -0400
  • 286f4cc8a8 Merge pull request #749 from broadinstitute/ldg_CGPfasterTests rpoplin 2014-10-15 15:53:48 -0400
  • 2b67e46e29 Adding total sensitivity option to ROCCurveNA12878 to help with Mauricio's analyses. Ryan Poplin 2014-10-15 12:46:32 -0400
  • 81482138ca Decrease interval on CGP integration test to reduce test execution time Laura Gauthier 2014-10-15 11:18:01 -0400
  • 0ad9daeac1 Merge pull request #747 from broadinstitute/gg_fixLicenseOmission rpoplin 2014-10-15 11:26:42 -0400
  • e7e8052f84 Updated license information Geraldine Van der Auwera 2014-10-14 13:42:56 -0400
  • 32bf46d8bf Merge pull request #748 from broadinstitute/rp_roc_curve_qual_field rpoplin 2014-10-14 14:30:52 -0400
  • 9680511cc3 In ROCCurveNA12878, if VQSLOD value is not present default to using the QUAL field instead to rank the variants. Ryan Poplin 2014-10-14 12:15:23 -0400
  • 426907ddd0 Merge pull request #744 from broadinstitute/gg_gatkdocs_annots_and_GSON rpoplin 2014-10-14 11:41:16 -0400
  • d259f3c84f Merge pull request #745 from broadinstitute/ldg_VariantAnnotatorDocs ldgauthier 2014-10-10 14:11:24 -0400
  • 22a3c6e556 Merge pull request #742 from broadinstitute/rhl_prob_thresh_param_arg jmthibault79 2014-10-10 12:55:01 -0400
  • 0ecb85d321 Added docs to VariantFiltration is accordance with new htsjdk changes. Fixed typo in VariantAnnotator docs. Laura Gauthier 2014-06-03 14:41:32 -0400
  • 36c27155af Made the threshold for the probability of a state being active a command line argument Ron Levine 2014-10-02 14:25:49 -0400
  • 4e099c1f44 Merge pull request #741 from broadinstitute/rhl_activiteregion_read_limits_args jmthibault79 2014-10-09 18:49:22 -0400
  • 645d418015 Changed hardcoded downsampling max/min coverage values to parameters Ron Levine 2014-10-01 20:26:41 -0400
  • 3f21f63161 Output JSON version of docs for Galaxy Geraldine Van der Auwera 2014-08-18 17:35:51 -0400
  • 58ca51e255 Switch GATKDocs publishing to new gsaweb VM Geraldine Van der Auwera 2014-09-02 06:24:10 +0100
  • 1cbf37c539 Merge pull request #739 from broadinstitute/rp_KB_reviews rpoplin 2014-10-01 09:53:08 -0400
  • b0481ced87 Merge pull request #738 from broadinstitute/vrr_slow_integration_test_due_to_general_ploidy_exact_af_calculator rpoplin 2014-10-01 09:52:04 -0400
  • a3ad6f63bd Reduce execution time of various integration tests Valentin Ruano-Rubio 2014-09-29 21:21:59 -0400
  • d609b2cdbb Adding manual review. Ryan Poplin 2014-09-30 12:53:55 -0400
  • 329bd081b7 Merge pull request #736 from broadinstitute/rhl_remove_line rpoplin 2014-09-29 15:03:55 -0400
  • d21ea126c4 Merge pull request #735 from broadinstitute/vrr_fix_qual_calculation_independent_exact_af_calculator rpoplin 2014-09-29 14:57:04 -0400
  • ff887f5674 Merge pull request #737 from broadinstitute/rp_VariantContextUtils_warning_message rpoplin 2014-09-29 14:49:32 -0400
  • 1c9d60c9a0 removed an unneed import that broke maven Ron Levine 2014-09-29 12:57:33 -0400
  • ac1a397024 This warning message actually happens all the time in AssessNA12878 when we subset down to biallelic events but I've verified that it is working as intended. Moving the logging level up to debug. Ryan Poplin 2014-09-29 11:40:10 -0400
  • 311b6815b3 Fixed the QUAL calculation of the EXACT_INDEPENDENT. Valentin Ruano-Rubio 2014-09-24 13:29:15 -0400
  • f7fc9cd839 Merge pull request #734 from broadinstitute/vrr_fix_mleac_general_ploidy_exact_af_calculator Valentin Ruano Rubio 2014-09-24 11:52:37 -0400
  • 0e52b8ba5a Fixed MLEAC and QUAL inaccuracy in GeneralPloidyExactAFCalculator. Valentin Ruano-Rubio 2014-09-22 15:15:38 -0400
  • 2da9bf7d09 Merge pull request #733 from broadinstitute/pd_allow_untrimmed_format Eric Banks 2014-09-17 23:34:09 -0400
  • 1482a53aba Added -writeFullFormat engine-level argument * This argument forces GATK to always write every record in the VCF format field, even if some records at the end are missing and could be removed * Revved htsjdk and picard * PT 70993484 Phillip Dexheimer 2014-09-16 21:16:39 -0400
  • 7cbb773c8f Merge pull request #731 from broadinstitute/vrr_omniploidy_afcalc_base Valentin Ruano Rubio 2014-09-12 16:30:31 -0400
  • f6cb83d476 Renamed AFCalc to AFCalculator for a better class naming Valentin Ruano-Rubio 2014-09-10 13:48:59 -0400
  • 95b45443ae Updated test according to changes in the AF calculator framework. Valentin Ruano-Rubio 2014-09-10 13:42:57 -0400
  • 3cdeab6e9e GenotypingEngines and walkers now use AFCalc(ulator) providers rathern than instanciate their own (fixed) calculators directly. Valentin Ruano-Rubio 2014-09-10 13:37:21 -0400
  • 935bd1394b AFCalculatorProvider components to allow for dynamic instantiation of different AFCalc(ulators) to cope with dynamic ploidy and max-alt-allele counts (the latter not used for now). Valentin Ruano-Rubio 2014-09-10 13:27:44 -0400
  • ce8e93fa51 Made the AF prior probability distribution dynamic respect to the total-ploidy (added ploidy accross samples). Valentin Ruano-Rubio 2014-09-10 13:20:03 -0400