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  • a75043b207 When git describe fails use "exported" instead of "unknown". Khalid Shakir 2014-02-18 02:17:48 +0800
  • 4670c87313 Fixed mvn run for packagetests over external-example. Khalid Shakir 2014-02-17 16:43:40 +0800
  • 70ecce2a0f Fixed scope for test-jar depedencies. Khalid Shakir 2014-02-15 16:46:44 +0800
  • a567a4d42c Merge pull request #530 from broadinstitute/vrr_gvcf_enabling_allele_trimming Valentin Ruano Rubio 2014-02-20 04:26:25 -0500
  • 463af7143f Activate reverse allele trimming in GVCF Valentin Ruano-Rubio 2014-02-19 20:19:09 -0500
  • 132e2429c8 Merge pull request #529 from broadinstitute/eb_fix_gvcf_writer_missing_blocks Eric Banks 2014-02-20 02:37:32 -0500
  • 53a7d5cbae Fixing a bug in the GVCF writer. Eric Banks 2014-02-20 00:53:13 -0500
  • 235f0c6fa0 Merge pull request #528 from broadinstitute/eb_fix_cat_variants_usage_message Eric Banks 2014-02-19 22:45:22 -0500
  • 341d1bf2dd Fix the usage message for CatVariants to make it accurate. It just hit a user on our forum... Eric Banks 2014-02-19 20:42:08 -0500
  • 6edebcb4ce Merge pull request #526 from broadinstitute/vrr_genotype_gvcf_untrimmed_alleles Valentin Ruano Rubio 2014-02-19 19:22:48 -0500
  • c167fb5fdf Fixing GenotypesGVCF. Valentin Ruano-Rubio 2014-02-14 16:34:13 -0500
  • 6963bf6c91 Merge pull request #527 from broadinstitute/dr_update_internal_build_script_for_maven droazen 2014-02-18 16:16:17 -0500
  • a3110b17a7 Update script to release jars for internal use for maven, and add Queue jar David Roazen 2014-02-18 15:32:10 -0500
  • 95c85b8105 Merge pull request #523 from broadinstitute/rp_random_forest_vqsr Eric Banks 2014-02-17 15:07:34 -0500
  • 43c20264b0 Initial commit of the random forest classifier. Ryan Poplin 2013-12-01 15:51:34 -0500
  • cb2d937a34 Merge pull request #525 from broadinstitute/ks_external_test_fix kshakir 2014-02-15 16:17:26 +0800
  • a505db79f5 Fixed build bug in ./ant-bridge.sh unittest -Dsingle=..., due to external-example. pipeline.run property no longer required to be passed by test executor. Khalid Shakir 2014-02-15 13:52:20 +0800
  • 688792c5b0 Merge pull request #520 from broadinstitute/jt_fix_failing_tests_post_maven droazen 2014-02-14 14:02:17 -0500
  • 1e82f117ad Merge pull request #518 from broadinstitute/ks_skashin_gatkdocs_arguments droazen 2014-02-14 13:57:19 -0500
  • f6022a944b Merge pull request #513 from broadinstitute/eb_clean_up_genotype_posteriors Eric Banks 2014-02-14 13:50:46 -0500
  • 3724d4e5f3 Various small fixes for CalculateGenotypePosteriors based on feedback from guys in Ben Neale's group. Eric Banks 2014-02-10 09:36:11 -0500
  • 8b136d53b9 Merge pull request #524 from broadinstitute/ks_symlink_bin_jar kshakir 2014-02-15 02:32:59 +0800
  • c64131e9fd Updated nightly tar of gatkdocs based on comments by droazen. Khalid Shakir 2014-02-15 02:27:53 +0800
  • cb7ad01202 Re-enable the relevant tests Joel Thibault 2014-02-14 12:34:08 -0500
  • 7215bfe825 Merge pull request #522 from broadinstitute/ks_build_external_example kshakir 2014-02-15 01:29:38 +0800
  • bc9ac93b6c Adding the external example to the build. Khalid Shakir 2014-02-09 17:05:51 +0800
  • 2e99a6ecf8 Create symlinks target/GenomeAnalysisTK.jar and target/Queue.jar during package phase. Khalid Shakir 2014-02-15 01:12:32 +0800
  • c8a5007c85 Add a comment to the method where the error appears Joel Thibault 2014-02-14 11:40:22 -0500
  • ec16439387 Clear the ReadCovariates keysCache before runs of individual Unit Tests - normal runs have a constant covariate count, so this is not necessary Joel Thibault 2014-02-13 16:23:47 -0500
  • 07a1d55209 Merge pull request #521 from broadinstitute/rp_apply_recalibration_qscript Ryan Poplin 2014-02-14 10:13:15 -0500
  • 9f26ad594e New qscript to run ApplyRecalibration in parallel. Ryan Poplin 2014-02-13 15:50:22 -0500
  • 16e82b8c2c Merge pull request #519 from broadinstitute/ks_nc6_checkpoint_patch kshakir 2014-02-14 21:47:34 +0800
  • 7ae19953f5 Squashed commit of the following: Nicholas Clarke 2014-02-14 09:35:06 +0000
  • 602fc0ca4d Merge pull request #509 from broadinstitute/ldg_empty_bam_list_error Eric Banks 2014-02-14 08:27:20 -0500
  • 29bb3d4dc1 Check for empty BAM lists in command line input Laura Gauthier 2014-02-12 10:20:28 -0500
  • 225ee4880b Using new parameters via skashin to run gatkdocs in the maven conventional subdirectory. Updated path for output gatkdocs in nightly build script. Removed patch in plugin manager that contained a workaround for gatkdocs running in the top level directory. Khalid Shakir 2014-02-14 15:57:21 +0800
  • 1b3ac95798 Added the following arguments: -settings-dir -destination-dir -forum-key-path skashin 2014-02-13 21:55:14 -0500
  • 7095a60c8e Merge pull request #516 from broadinstitute/dr_reenable_tests_failing_due_to_java_update Eric Banks 2014-02-13 21:05:18 -0500
  • 238bf4e71d Merge pull request #515 from broadinstitute/ks_picard_maven_update_svn kshakir 2014-02-13 23:32:56 +0800
  • 78e492e17c Removed use of rt.jar now that com.sun annotations are no longer used. Khalid Shakir 2014-02-13 12:16:26 +0800
  • 7457fc2c6d Switched svn up invocation from buildnumber-maven-plugin to maven-antrun-plugin, due to mixed revisions by running svn up <dir> instead of just svn up. Removed unused scm element that was required by buildnumber. Khalid Shakir 2014-02-13 03:53:05 +0800
  • 1c3c20ece3 Merge pull request #514 from broadinstitute/dr_update_nightly_build_script_for_maven droazen 2014-02-12 17:43:40 -0500
  • 0d07121a8d Update nightly build script for maven David Roazen 2014-02-12 16:07:09 -0500
  • a1f191ce45 Merge pull request #507 from jsilter/master Eric Banks 2014-02-12 16:15:09 -0500
  • 4b4b93ad1b Re-enable tests that were failing post-maven due to changes in Java's Math.pow() implementation David Roazen 2014-02-12 14:51:51 -0500
  • 400800e676 Add ability to read dbSpec over http Jacob Silterra 2014-02-12 16:02:31 -0500
  • 10716ca17b Merge pull request #510 from broadinstitute/dr_phone_home_script_updates Eric Banks 2014-02-12 15:40:41 -0500
  • 5bde7fbf37 Merge pull request #511 from broadinstitute/dr_enable_exclusions_in_maven_package_tests Eric Banks 2014-02-12 15:38:39 -0500
  • b8db5a9502 Merge pull request #512 from broadinstitute/jt_multi_allele_fix Eric Banks 2014-02-12 15:38:02 -0500
  • bc3d1addee Merge pull request #508 from broadinstitute/rp_ROCCurveNA12878_plot_filtered_status Eric Banks 2014-02-12 15:33:15 -0500
  • ef87b051b0 Rev Picard to 1.107.1683 (4 jars) Joel Thibault 2014-02-12 13:37:29 -0500
  • 6f12c8b0dc Exclude all transitive dependencies in maven package-tests David Roazen 2014-02-12 14:59:05 -0500
  • 3b8670490d Use s3funnel instead of s3cmd for listing/downloading/deleting David Roazen 2014-01-23 06:44:21 -0500
  • 9ef3f5663f Phone home script updates David Roazen 2013-12-03 13:20:16 -0500
  • cc9477aedb Minimal test for the multi-allelic reordering bug Joel Thibault 2014-02-11 13:12:54 -0500
  • 1fcca8c5c0 Adding the filter field to the output of ROCCurveNA12878 Ryan Poplin 2014-02-12 12:46:30 -0500
  • 6facf695ab Merge pull request #506 from broadinstitute/eb_quick_fixes_to_single_sample_pipeline Eric Banks 2014-02-12 11:30:48 -0500
  • 300b474c96 Several improvements to the single sample combining steps. Eric Banks 2014-02-12 09:02:02 -0500
  • ff8c9575b0 Merge pull request #505 from broadinstitute/ks_build_na12878kb-utils Eric Banks 2014-02-12 10:10:52 -0500
  • 403ce7bfb7 Ported na12878kb.jar assembly from Ant's build.xml to Maven at request of jsilter Khalid Shakir 2014-02-12 05:44:11 +0800
  • 3cfcfa4fa0 Merge pull request #504 from broadinstitute/dr_enable_kb_tests_in_maven droazen 2014-02-11 15:32:24 -0500
  • 95e1402d21 Add ability to run *KnowledgeBaseTests to maven David Roazen 2014-02-11 14:03:26 -0500
  • cc9a3b68fc Merge pull request #503 from broadinstitute/ks_maven_gatkdocs_patch droazen 2014-02-11 13:28:24 -0500
  • 96e29d3d94 Merge pull request #500 from broadinstitute/eb_make_qd_more_robust Eric Banks 2014-02-11 12:57:50 -0500
  • 303a60c8c6 Adding smarts to the QD annotation: when the AD annotation is present for a given genotype then we only use its depth for QD if the variant depth > 1. Eric Banks 2014-02-10 15:31:59 -0500
  • 1666bb7e3a Patched PluginManager to ignore null classes, that will allow gatkdocs to build successfully when running from the source root directory, due to its hardcoded paths. Khalid Shakir 2014-02-12 00:48:58 +0800
  • b33d9d9105 Merge pull request #502 from broadinstitute/eb_make_combine_gvcfs_faster Eric Banks 2014-02-11 09:03:16 -0500
  • 2e36dd9001 Refactoring of CombineGVCFs to make it run a lot faster. Eric Banks 2014-02-11 03:18:52 -0500
  • 316501b32e Fixed denominator in profiling Karthik Gururaj 2014-02-10 10:11:03 -0800
  • d081c19178 Minor: added support in C++ sandbox to choose implementation and check from command line Karthik Gururaj 2014-02-09 18:05:35 -0800
  • b81494b704 Merge pull request #499 from broadinstitute/eb_fix_ad_updates Ryan Poplin 2014-02-09 17:55:00 -0500
  • abb67cfa5e Fixed bug in generating AD values when new alleles are present for genotpying GVCFs. Eric Banks 2014-02-09 15:15:19 -0500
  • c2a2484a18 Merge pull request #498 from broadinstitute/ks_delete_pricard_private Eric Banks 2014-02-09 10:27:48 -0500
  • 12bb6fd361 Removed use of picard private. Updated picard-maven script to tag locally modified builds with -SNAPSHOT. Removed old picard jars. Khalid Shakir 2014-02-09 09:08:47 +0800
  • 597cc88f33 Merge pull request #497 from broadinstitute/eb_remove_ac0_alleles_PT65118652 Eric Banks 2014-02-08 23:46:23 -0500
  • abef6cfcb6 Removing parameters that were incorrectly copied over from RegenotypeVariants. Eric Banks 2014-02-08 23:24:46 -0500
  • e9189cd471 Merge pull request #496 from broadinstitute/eb_remove_test_for_blocksize Eric Banks 2014-02-08 21:29:02 -0500
  • 659a9f0e79 Removing the test for BLOCK_SIZE since we no longer emit it Eric Banks 2014-02-08 21:28:07 -0500
  • a33d7ace11 Merge pull request #495 from broadinstitute/ks_increase_scala_memory Eric Banks 2014-02-08 21:13:26 -0500
  • 4decb49ecb Merge pull request #494 from broadinstitute/vrr_reference_model_nocall_bugfix Eric Banks 2014-02-08 21:12:45 -0500
  • 4e0f7521f2 Made scala.maxmemory an argument, and defaulted it to 1g. Khalid Shakir 2014-02-09 09:24:44 +0800
  • a03d83579b Matrices in baseline C++ (no vector) implementation of PairHMM are now allocated on heap using "new". Stack allocation led to program crashes for large matrix sizes. Karthik Gururaj 2014-02-07 23:22:05 -0800
  • bf630abe88 Fixed nocall (./.) without PLs bug in GVCF output Valentin Ruano-Rubio 2014-02-07 15:24:49 -0500
  • 20a46e4098 Check only for SSE 4.1 (rather than SSE 4.2) when trying to use the SSE implementation of PairHMM Karthik Gururaj 2014-02-07 15:19:55 -0800
  • dc44b64ad8 1. Added support for building the PairHMM vector library into build.xml. The library is compiled using makefile and copied into the directory: build/java/classes/org/broadinstitute/sting/utils/pairhmm/ 2. Bundled the library into StingUtils.jar. Unpacked and loaded at runtime without the need to set java.library.path Karthik Gururaj 2014-02-07 13:13:59 -0800
  • 8c922be684 Merge pull request #491 from broadinstitute/eb_get_AD_back_from_gvcfs Eric Banks 2014-02-07 12:50:01 -0500
  • d689f61005 Fixed up some of the genotype-level annotations being propogated in the single sample HC pipeline. Eric Banks 2014-02-07 11:36:49 -0500
  • 0a1385a4d9 Merge pull request #493 from broadinstitute/eb_fix_failing_merge_for_tim Eric Banks 2014-02-07 12:43:40 -0500
  • 67ed0d2403 The UG engine can return a null VC if there are tons of alt alleles, causing Tim's merge jobs to fail. Pushing the null check up so that it doesn't error out in such cases. Eric Banks 2014-02-07 12:41:20 -0500
  • 335483bb53 Merge pull request #492 from broadinstitute/eb_fix_failing_unit_tests Eric Banks 2014-02-07 12:25:10 -0500
  • db68d3fa10 Fixing failing unit tests Eric Banks 2014-02-07 12:24:14 -0500
  • 8e87e083ff Merge pull request #490 from broadinstitute/vrr_reference_model_unsorted_records_bugfix Valentin Ruano Rubio 2014-02-07 12:21:12 -0500
  • 4a3c8e68fa Fixed out of order non-variant gVCF entries when trimming is active. Valentin Ruano-Rubio 2014-02-06 17:45:50 -0500
  • 369fbd4439 Merge pull request #489 from broadinstitute/eb_hierarchical_gvcf_merger Eric Banks 2014-02-07 08:50:39 -0500
  • eb463b505d Remove a whole bunch of unused annotations from gVCF output. Eric Banks 2014-02-06 16:17:15 -0500
  • 2648219c42 Implementation of a hierarchical merger for gVCFs, called CombineGVCFs. Eric Banks 2014-02-06 01:32:24 -0500
  • 7815c30df8 Adding comments to pairhmm-template-kernel mghodrat 2014-02-06 20:13:06 -0800
  • b729fc0136 1. Split main JNI function into initializeTestcases, compute_testcases and releaseReads 2. FTZ enabled 3. Cleaner profiling code Karthik Gururaj 2014-02-06 14:35:32 -0800
  • 71b47a6148 Rename CombineReferenceCalculationVariants to GenotypeGVCFs Eric Banks 2014-02-05 22:01:12 -0500
  • b2b44c335f Merge pull request #488 from broadinstitute/ks_mvn_serial_test_updates droazen 2014-02-06 15:12:08 -0500