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  • 3847de5290 run_parallel_tests: detect farm glitches David Roazen 2013-03-12 23:26:33 -0400
  • c289103c7d Merge pull request #102 from broadinstitute/dr_parallel_test_runner_improvements Mark DePristo 2013-03-12 18:04:55 -0700
  • 7d06d15f3c parallel test runner: support multiple kinds of tests per run, logging, improved script output David Roazen 2013-03-12 17:55:15 -0400
  • b3f67899b5 Merge pull request #101 from broadinstitute/dr_fix_failing_parallel_tests Mark DePristo 2013-03-12 14:11:02 -0700
  • cdb1fa1105 Fix more tests that fail when run in parallel on the farm David Roazen 2013-03-12 13:41:29 -0400
  • 4403e3572a Merge pull request #94 from broadinstitute/gg_gatkdoc_docfixes_GSATDG-111 MauricioCarneiro 2013-03-12 13:02:35 -0700
  • 3a16ba04d4 Merge pull request #97 from broadinstitute/eb_refactor_sliding_window MauricioCarneiro 2013-03-12 12:27:26 -0700
  • dcdd6e3e60 Merge pull request #96 from broadinstitute/md_assess_only_reviewed droazen 2013-03-12 10:29:07 -0700
  • f972963918 Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) Geraldine Van der Auwera 2013-03-05 13:58:50 -0500
  • 01c2e6e9fa Merge pull request #99 from broadinstitute/ami-fix-compilationError-LScallingPipeline Mark DePristo 2013-03-12 07:47:57 -0700
  • e2d4d1da20 fix compilation error in ReduceReadsScript (missing import) Ami Levy-Moonshine 2013-03-11 11:02:53 -0400
  • eaf9c30257 fix compilation error (change from org.broadinstitute.variant.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED to GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED) Ami Levy-Moonshine 2013-03-11 10:55:28 -0400
  • 72f9abfcab Merge pull request #98 from broadinstitute/rp_hc_glm_both Mark DePristo 2013-03-12 07:09:43 -0700
  • 05e69b6294 Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug. Eric Banks 2013-03-08 10:28:11 -0500
  • 08db3b5155 Add mode to AssessNA12878 that will only consider reviewed sites Mark DePristo 2013-03-05 15:41:12 -0500
  • c96fbcb995 Use the indel heterozygosity prior when calling indels with the HC Ryan Poplin 2013-03-11 14:12:43 -0400
  • 7dce4f8630 Merge pull request #95 from broadinstitute/dr_parallel_tests_with_job_arrays Mark DePristo 2013-03-11 10:57:39 -0700
  • df9821614c run_parallel_tests: add job array support David Roazen 2013-03-11 12:32:56 -0400
  • 508b58376c Merge pull request #93 from broadinstitute/gda_ancient_dna Eric Banks 2013-03-10 17:57:28 -0700
  • ec8617bc9b Removing mark duplicates from the quick processing pipeline Mauricio Carneiro 2013-03-10 17:24:22 -0400
  • 695723ba43 Two features useful for ancient DNA processing. Ancient DNA sequencing data is in many ways different from modern data, and methods to analyze it need to be adapted accordingly. Feature 1: Read adaptor trimming. Ancient DNA libraries typically have very short inserts (in the order of 50 bp), so typical Illumina libraries sequenced in, say, 100bp HiSeq will have a large adaptor component being read after the insert. If this adaptor is not removed, data will not be aligneable. There are third party tools that remove adaptor and potentially merge read pairs, but are cumbersome to use and require precise knowledge of the library construction and adaptor sequence. -- New walker ReadAdaptorTrimmer walks through paired end data, computes pair overlap and trims auto-detected adaptor sequence. -- Unit tests added for trimming operation. -- Utility walker (may be retired later) DetailedReadLengthDistribution computes insert size or read length distribution stratified by read group and mapping status and outputs a GATKReport with data. -- Renamed MaxReadLengthFilter to ReadLengthFilter and added ability to specify minimum read length as a filter (may be useful if, as a consequence of adaptor trimming, we're left with a lot of very short reads which will map poorly and will just clutter output BAMs). Guillermo del Angel 2013-02-18 20:00:46 -0500
  • 21a6b4add2 Merge pull request #92 from broadinstitute/yf_allow_spaces_in_sampleID_in_contam_file droazen 2013-03-07 12:07:51 -0800
  • baad965a57 - Changed loadContaminationFile file parser to delimit by tab only. This allows spaces in sampleIDs, which apparently are allowed. - This was needed since samples with spaces in their names are regularly found in the picard pipeline. - Modified the tests to account for this (removed spaces from the good tests, and changed the failing tests accordingly) - Cleaned up the unit tests using a @DataProvider (I'm in love...). - Moved AlleleBiasedDownsamplingUtilsUnitTest to public to match location of class it is testing (due to the way bamboo operates) Yossi Farjoun 2013-03-06 11:15:30 -0500
  • ecb2599cde Merge pull request #91 from broadinstitute/dr_fix_failing_parallel_tests Mark DePristo 2013-03-06 11:47:36 -0800
  • 3ab78543a7 Fix tests that were consistently or intermittently failing when run in parallel on the farm David Roazen 2013-03-05 01:27:36 -0500
  • 7d833256e8 Merge pull request #90 from broadinstitute/eb_allow_read_transform_ordering Mark DePristo 2013-03-06 09:52:26 -0800
  • 3759d9dd67 Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. Eric Banks 2013-03-05 15:57:44 -0500
  • 446cd61f7e Merge pull request #84 from broadinstitute/eb_allelic_primitives Mark DePristo 2013-03-06 09:02:21 -0800
  • dadc079dbc Merge pull request #89 from broadinstitute/mc_fix_output_annotation_GSA-820 Mark DePristo 2013-03-06 09:01:20 -0800
  • 802ce76209 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-03-06 10:18:47 -0500
  • 5577715ae2 Have all significant XHMM commands be run with LongRunTime Menachem Fromer 2013-03-06 10:18:23 -0500
  • 64a9ccded6 Merge pull request #77 from broadinstitute/mc_postqc_tsca Mark DePristo 2013-03-06 07:13:10 -0800
  • 928f646afd Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-03-06 10:01:29 -0500
  • 78721ee09b Added new walker to split MNPs into their allelic primitives (SNPs). Eric Banks 2013-03-04 14:13:42 -0500
  • e2d41f0282 Turning @Output required to false Mauricio Carneiro 2013-03-05 17:25:52 -0500
  • f10723df3b Merge pull request #85 from broadinstitute/md_simple_kb_report delangel 2013-03-05 10:39:39 -0800
  • 2be57fbcfb Merged bug fix from Stable into Unstable Eric Banks 2013-03-05 13:28:46 -0500
  • 5e89f01e10 Don't allow the use of compressed (.gz) references in the GATK. Eric Banks 2013-03-05 13:28:19 -0500
  • 92ac9e7f65 AssessNA12878 now emits a simplified assessment table by default Mark DePristo 2013-03-01 15:41:30 -0500
  • b5a07da04c Merge pull request #88 from broadinstitute/eb_fix_pairHMM_from_stable Eric Banks 2013-03-05 06:07:50 -0800
  • bbbaf9ad20 Revert push from stable (I forgot that pushing from stable overwrites current unstable changes) Eric Banks 2013-03-05 09:06:02 -0500
  • a037423225 Merged bug fix from Stable into Unstable Eric Banks 2013-03-05 09:03:48 -0500
  • 7e1bfd6a7c Included an accidental change from unstable into the previous push Eric Banks 2013-03-05 09:03:31 -0500
  • 3e118a5b41 Adding interval list to Postcalling QC script Mauricio Carneiro 2013-02-28 11:51:43 -0500
  • 74a5cd5956 run_parallel_tests: archive working directories for completed runs David Roazen 2013-03-05 05:49:25 -0500
  • 754226907e run_parallel_tests.sh: improved test class search and post-test cleanup David Roazen 2013-03-05 04:22:51 -0500
  • bd4e4f4ee3 Merged bug fix from Stable into Unstable Eric Banks 2013-03-04 23:24:44 -0500
  • b715218bfe Fix for mismatching indel quals erro: need to adjust for softclips just like we do for bases and normal quals. Eric Banks 2013-03-04 23:23:18 -0500
  • 1b7164ccdb Merge pull request #86 from broadinstitute/mc_fix_exception_messages Mark DePristo 2013-03-04 13:55:00 -0800
  • d0c8105387 Cleaning up hilarious exception messages Mauricio Carneiro 2013-03-04 16:47:45 -0500
  • ce7554e9d6 Merged bug fix from Stable into Unstable Ryan Poplin 2013-03-04 12:36:04 -0500
  • 0697594778 Active regions that don't contain any usable reads should just be skipped over instead of throwing an IllegalStateException. Ryan Poplin 2013-03-04 12:35:40 -0500
  • b3ecbb011d Merge pull request #81 from broadinstitute/md_hc_bam_writing Ryan Poplin 2013-03-04 06:39:19 -0800
  • 42d3919ca4 Expanded functionality for writing BAMs from HaplotypeCaller Mark DePristo 2013-02-22 15:22:43 -0500
  • ec3bf9f362 Adding 1mb of 2x250 bp PCR-free reads to private testdata Mark DePristo 2013-03-01 13:37:48 -0500
  • b1ea2f6125 Merge pull request #83 from broadinstitute/dr_gatk_jar_with_private_GSA-803 Mark DePristo 2013-03-01 13:15:57 -0800
  • 2a1a20fc9d Parallel tests: switch working directory from /humgen/gsa-scr1 to /humgen/gsa-hpprojects David Roazen 2013-03-01 16:11:29 -0500
  • a0be74c2ef Ant target to package a GATK jar with private included David Roazen 2013-03-01 15:33:59 -0500
  • 3f7d888ea5 run_parallel_tests.sh: further improvements David Roazen 2013-03-01 14:59:10 -0500
  • 0cff9b8027 Merge pull request #82 from broadinstitute/dr_split_long_integration_test_classes Mark DePristo 2013-03-01 11:07:23 -0800
  • c5c99c8339 Split long-running integration test classes into multiple classes David Roazen 2013-03-01 13:06:58 -0500
  • 6204e6ccc9 Merge pull request #76 from broadinstitute/md_kb_bugfix_GSA-795 depristo 2013-03-01 10:52:16 -0800
  • c05d1352b1 Merge pull request #80 from broadinstitute/eb_cleanup_genomelocsortedset_GSA-775 depristo 2013-03-01 08:35:20 -0800
  • ebd5404124 Fixed the add functionality of GenomeLocSortedSet. Eric Banks 2013-02-28 13:46:49 -0500
  • 6a77eee5f4 parallel tests script: pass in bamboo build number to make globally unique working directories for each run David Roazen 2013-02-28 18:06:18 -0500
  • 2a7f55ae45 Further run_parallel_tests.sh quick fixes David Roazen 2013-02-28 17:31:29 -0500
  • 394e8889f1 Fix silly typo in run_parallel_tests.sh script David Roazen 2013-02-28 17:15:32 -0500
  • e5fa1672c1 Merge pull request #79 from broadinstitute/dr_parallel_tests_prototype MauricioCarneiro 2013-02-28 14:12:37 -0800
  • e6ac94fd75 Experimental script to run tests using class-level parallelism on the farm David Roazen 2013-02-28 16:39:43 -0500
  • ca42be9788 Merge pull request #78 from broadinstitute/dr_pdfgen_bamboo_script_GSA-794 droazen 2013-02-28 11:48:41 -0800
  • b050d16b22 Trivial shell script for bamboo to trigger the website pdfgen script David Roazen 2013-02-28 14:45:25 -0500
  • 0931afab39 NA12878 KB performance improvement Mark DePristo 2013-02-28 10:34:15 -0500
  • 4095a9ef32 Bugfixes for AssessNA12878 Mark DePristo 2013-02-27 15:38:17 -0500
  • 92d6a4f441 Merge pull request #75 from broadinstitute/eb_missing_rg_error_GSA-407 depristo 2013-02-28 05:20:39 -0800
  • cac3f80c64 Merge pull request #73 from broadinstitute/eb_remove_nested_hashmap_GSA-732 depristo 2013-02-28 05:19:56 -0800
  • 12fc198b80 Added better error message for BAMs with bad read groups. * Split the cases into reads that don't have a RG at all vs. those with a RG that's not defined in the header. * Added integration tests to make sure that the correct error is thrown. * Resolved GSA-407. Eric Banks 2013-02-27 16:02:56 -0500
  • 45fc0ed261 Merge pull request #74 from broadinstitute/eb_update_rtc_docs_GSA-716 Eric Banks 2013-02-27 11:58:09 -0800
  • d2904cb636 Update docs for RTC. Eric Banks 2013-02-27 14:55:49 -0500
  • 97b332943b Merge pull request #64 from broadinstitute/md_agbt MauricioCarneiro 2013-02-27 11:41:04 -0800
  • 69b8173535 Replace uses of NestedHashMap with NestedIntegerArray. Eric Banks 2013-02-27 14:01:09 -0500
  • 4b1071a815 Merge pull request #68 from broadinstitute/aw_reduce_reads_perf Eric Banks 2013-02-27 10:03:36 -0800
  • c8368ae2a5 Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and replace with in-line primitive attributes. This is ugly but reduces heap overhead, and changes are localized. When used in conjunction with Mauricio's FastUtil changes it saves and additional 9% or so of execution time. Alec Wysoker 2013-02-26 16:23:12 -0500
  • 69f6d53494 Merge pull request #72 from broadinstitute/md_profile_hc_vs_ug_GSA-749 Ryan Poplin 2013-02-27 08:14:00 -0800
  • b987df5d8d GATKPerformanceOverTime now includes a mode to comparing HC & UG performance Mark DePristo 2013-02-04 15:48:16 -0500
  • 752f4335a5 Merged bug fix from Stable into Unstable David Roazen 2013-02-27 05:20:41 -0500
  • 2a7af43164 Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest David Roazen 2013-02-27 04:45:53 -0500
  • 6466463d5a Merged bug fix from Stable into Unstable David Roazen 2013-02-26 21:54:54 -0500
  • 12a3d7ecad Fix licenses on files modified in 2.4-1 David Roazen 2013-02-26 21:47:55 -0500
  • a53b4a7521 Merged bug fix from Stable into Unstable David Roazen 2013-02-26 21:41:13 -0500
  • 65d31ba4ad Fix runtime public -> protected dependencies in the test suite David Roazen 2013-02-26 21:11:13 -0500
  • dd338bebd0 Merge pull request #70 from broadinstitute/dr_nightly_build_script_adjustments droazen 2013-02-26 14:46:09 -0800
  • d2f4626bdd Nightly build script improvements David Roazen 2013-02-26 17:43:19 -0500
  • 7c3f8d384b Merge pull request #69 from broadinstitute/dr_nightly_build_script_GSATDG-78 depristo 2013-02-26 13:58:39 -0800
  • 3680879926 Shell script to release GATK nightly builds David Roazen 2013-02-26 16:15:37 -0500
  • 93205154b5 Merge pull request #63 from broadinstitute/eb_fix_pairhmm_unittest_GSA-776 depristo 2013-02-26 11:56:58 -0800
  • 734353e9df Merge pull request #60 from broadinstitute/mc_fastutil_GSATDG-83 Eric Banks 2013-02-26 11:56:41 -0800
  • 3ce0a32da7 Merge remote-tracking branch 'unstable/master' Eric Banks 2013-02-26 14:48:39 -0500
  • 7a7adb79f1 Merge pull request #67 from broadinstitute/dr_release_script_disable_validation Eric Banks 2013-02-26 11:25:01 -0800
  • 2cf0dc9939 Merge pull request #66 from broadinstitute/mc_retire_coveragebysample_walker_GSATDG-90 Eric Banks 2013-02-26 11:19:09 -0800
  • 2b13af042d Temporarily disable paranoid validation in the release scripts David Roazen 2013-02-26 14:17:39 -0500