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  • f42bdaee3c Merge pull request #133 from broadinstitute/chartl_fix_validation_site_selector_md5s MauricioCarneiro 2013-03-29 12:57:10 -0700
  • 74a17359a8 MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods that are tested), resulting in slightly different numbers of calls to the RNG, and ultimately different sets of selected variants. Chris Hartl 2013-03-29 14:52:10 -0400
  • ed98fc6a1f Merge pull request #131 from broadinstitute/gda_1000g_consensus_GSA-890 Mark DePristo 2013-03-29 08:03:14 -0700
  • 8fbf9c947f Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production: -- Added ability to trim common bases in front of indels before left-aligning. Otherwise, records may not be left-aligned if they have common bases, as they will be mistaken by complext records. -- Added ability to split multiallelic records and then left align them, otherwise we miss a lot of good left-aligneable indels. -- Motivated by this, renamed walker to LeftAlignAndTrimVariants. -- Code refactoring, cleanup and bring up to latest coding standards. -- Added unit testing to make sure left alignment is performed correctly for all offsets. -- Changed phase 3 HC script to new syntax. Add command line options, more memory and reduce alt alleles because jobs keep crashing. Guillermo del Angel 2013-03-22 18:25:47 -0400
  • b818a4f219 Merge pull request #130 from broadinstitute/chartl_genotype_concordance_and_mathutils MauricioCarneiro 2013-03-29 05:24:59 -0700
  • 73d1c319bf Rarely-occurring logic bugfix for GenotypeConcordance, streamlining and testing of MathUtils Chris Hartl 2013-03-28 23:25:28 -0400
  • a2b69790a6 Merge pull request #128 from broadinstitute/eb_rr_polyploid_compression_GSA-639 MauricioCarneiro 2013-03-28 06:39:43 -0700
  • e58d0a71e4 Merge pull request #129 from broadinstitute/md_hc_good_head_tail Ryan Poplin 2013-03-27 12:36:39 -0700
  • fde7d36926 Updating md5s due to changes in assembly graph creation algorithms and default parameter Mark DePristo 2013-03-26 22:07:25 -0400
  • 197d149495 Increase the maxNumHaplotypesInPopulation to 25 Mark DePristo 2013-03-26 21:00:04 -0400
  • 66910b036c Added new and improved suffix and node merging algorithms Mark DePristo 2013-03-25 18:37:25 -0400
  • 39f2e811e5 Increase max cigar elements from SW before failing path creation to 20 from 6 Mark DePristo 2013-03-25 18:38:12 -0400
  • b1b615b668 BaseGraph shouldn't implement getEdge -- no idea why I added this Mark DePristo 2013-03-25 18:31:23 -0400
  • a97576384d Fix bug in the HC not respecting the requested pruning Mark DePristo 2013-03-25 18:29:16 -0400
  • 78c672676b Bugfix for pruning and removing non-reference edges in graph Mark DePristo 2013-03-24 17:20:30 -0400
  • 12475cc027 Display the active MappingQualityFilter if mmq > 0 in the HaplotypeCaller Mark DePristo 2013-03-24 14:42:48 -0400
  • ad04fdb233 PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now Mark DePristo 2013-03-24 14:41:21 -0400
  • 2472828e1c HC bug fixes: no longer create reference graphs with cycles Mark DePristo 2013-03-22 23:42:44 -0400
  • 1917d55dc2 Bugfix for DeBruijnAssembler: don't fail when read length > haplotype length Mark DePristo 2013-03-22 22:58:25 -0400
  • 464e65ea96 Disable error correcting kmers by default in the HC Mark DePristo 2013-03-23 14:10:54 -0400
  • 593d3469d4 Refactored the het (polyploid) consensus creation in ReduceReads. Eric Banks 2013-03-15 12:20:23 -0400
  • 965043472a Vastly more powerful, cleaner graph simplification approach Mark DePristo 2013-03-22 08:30:49 -0400
  • 078c63654d Merge pull request #127 from broadinstitute/mc_callable_loci_with_reduce_reads Mark DePristo 2013-03-21 17:56:23 -0700
  • de832de03d Merge pull request #125 from broadinstitute/mc_fly_pipeline Mark DePristo 2013-03-21 13:11:53 -0700
  • eb33da6820 Added support to reduce reads to Callable Loci Mauricio Carneiro 2013-03-21 15:29:27 -0400
  • c15453542e Merge pull request #124 from broadinstitute/md_hc_lowmapq_read_filter Ryan Poplin 2013-03-21 12:00:28 -0700
  • b30deda7ee Merge pull request #123 from broadinstitute/rp_event_mapper_bug_GSA-877 Mark DePristo 2013-03-21 11:42:20 -0700
  • 7ae15dadbe HC now by default only uses reads with MAPQ >= 20 for assembly and calling Mark DePristo 2013-03-21 11:27:00 -0400
  • b9c331c2fa Bug fix in HC gga mode. Ryan Poplin 2013-03-21 10:59:34 -0400
  • 1a95ce5dcf Merge pull request #122 from broadinstitute/md_ceu_trio_calls_2x250_GSA-739 Ryan Poplin 2013-03-21 06:58:13 -0700
  • aa7f172b18 Cap the computational cost of the kmer based error correction in the DeBruijnGraph Mark DePristo 2013-03-20 22:40:10 -0400
  • d94b3f85bc Increase NUM_BEST_PATHS_PER_KMER_GRAPH in DeBruijnAssembler to 25 Mark DePristo 2013-03-20 20:56:58 -0400
  • 6d7d21ca47 Bugfix for incorrect branch diamond merging algorithm Mark DePristo 2013-03-20 15:57:10 -0400
  • 3a8f001c27 Misc. fixes upon pull request review Mark DePristo 2013-03-20 14:26:37 -0400
  • d3b756bdc7 BaseVertex optimization: don't clone byte[] unnecessarily Mark DePristo 2013-03-20 08:39:01 -0400
  • 5226b24a11 HaplotypeCaller instructure cleanup and unit testing Mark DePristo 2013-03-19 18:09:23 -0400
  • 2e36f15861 Update md5s to reflect new downsampling and assembly algorithm output Mark DePristo 2013-03-19 16:22:06 -0400
  • 1fa5050faf Cleanup, unit test, and optimize KBestPaths and Path Mark DePristo 2013-03-19 14:33:09 -0400
  • 98c4cd060d HaplotypeCaller now uses SeqGraph instead of kmer graph to build haplotypes. Mark DePristo 2013-03-14 10:03:04 -0400
  • 0f4328f6fe Basic kmer error correction algorithm xfor the HaplotypeCaller Mark DePristo 2013-03-08 13:10:15 -0500
  • 53a904bcbd Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads Mark DePristo 2013-03-08 11:28:22 -0500
  • ffea6dd95f HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping Mark DePristo 2013-03-18 17:06:32 -0400
  • a8fb26bf01 A generic downsampler that reduces coverage for a bunch of reads Mark DePristo 2013-03-06 21:39:18 -0500
  • 752440707d AlignmentUtils.calcNumDifferentBases computes the number of bases that differ between a reference and read sequence given a cigar between the two. Mark DePristo 2013-03-06 13:52:53 -0500
  • a783f19ab1 Fix for potential HaplotypeCaller bug in annotation ordering Mark DePristo 2013-03-06 13:45:53 -0500
  • 559a4bc05d Updating general calling pipeline to work with newer HC and UG arguments and filtering Mark DePristo 2013-03-03 18:29:47 -0500
  • 1fae750ebe Merge pull request #120 from broadinstitute/aw_reduce_reads_clear_name_cache Eric Banks 2013-03-20 19:47:42 -0700
  • 7e29beadff Merge pull request #121 from broadinstitute/gda_hc_gls_for_1000g_GSA-878 Mark DePristo 2013-03-20 14:08:10 -0700
  • ea01dbf130 Fix to issue encountered when running HaplotypeCaller in GGA mode with data from other 1000G callers. In particular, someone produced a tandem repeat site with 57 alt alleles (sic) which made the caller blow up. Inelegant fix is to detect if # of alleles is > our max cached capacity, and if so, emit an informative warning and skip site. -- Added unit test to UG engine to cover this case. -- Commit to posterity private scala script currently used for 1000G indel consensus (still very much subject to changes). GSA-878 #resolve Guillermo del Angel 2013-03-19 15:26:50 -0400
  • 470746c907 Merge pull request #117 from broadinstitute/gg_handling_deprecated_tools_45941819 MauricioCarneiro 2013-03-20 07:31:33 -0700
  • d70bf64737 Created new DeprecatedToolChecks class --Based on existing code in GenomeAnalysisEngine --Hashmaps hold mapping of deprecated tool name to version number and recommended replacement (if any) --Using FastUtils for maps; specifically Object2ObjectMap but there could be a better type for Strings... --Added user exception for deprecated annotations --Added deprecation check to AnnotationInterfaceManager.validateAnnotations --Run when annotations are initialized --Made annotation sets instead of lists Geraldine Van der Auwera 2013-03-15 16:41:14 -0400
  • 6b4d88ebe9 Created ListAnnotations utility (extends CommandLineProgram) --Refactored listAnnotations basic method out of VA into HelpUtils --HelpUtils.listAnnotations() is now called by both VA and the new ListAnnotations utility (lives in sting.tools) --This way we keep the VA --list option but we also offer a way to list annotations without a full valid VA command-line, which was a pain users continually complained about --We could get rid of the VA --list option altogether ...? Geraldine Van der Auwera 2013-03-15 16:34:29 -0400
  • 95a9ed853d Made some documentation updates & fixes --Mostly doc block tweaks --Added @DocumentedGATKFeature to some walkers that were undocumented because they were ending up in "uncategorized". Very important for GSA: if a walker is in public or protected, it HAS to be properly tagged-in. If it's not ready for the public, it should be in private. Geraldine Van der Auwera 2013-03-15 13:26:05 -0400
  • bccc9d79e5 Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash. Alec Wysoker 2013-03-19 14:03:40 -0400
  • c813259283 Merge pull request #119 from broadinstitute/md_assessn12878_bugfixes Ryan Poplin 2013-03-19 05:11:50 -0700
  • d4f873f664 Revert "github webhook handler: convert from daemon to cron job" David Roazen 2013-03-19 03:45:24 -0400
  • ff79118379 github webhook handler: convert from daemon to cron job David Roazen 2013-03-19 02:40:01 -0400
  • f9ad8d4325 Merged bug fix from Stable into Unstable David Roazen 2013-03-19 01:23:58 -0400
  • 532efad8cd Release scripts: small changes to reduce intermittent failures David Roazen 2013-03-19 00:53:47 -0400
  • d7bec9eb6e AssessNA12878 bugfixes Mark DePristo 2013-03-18 12:55:58 -0400
  • a36e2b8f9d Merge pull request #118 from broadinstitute/ami-typoInCoveredByNSamplesSites Eric Banks 2013-03-18 11:10:10 -0700
  • 0e9c1913ff fix typos in argument docs and in printed output in CoveredByNSamplesSites and rewrite an unaccurate comment Ami Levy-Moonshine 2013-03-18 10:46:27 -0400
  • 2b80068164 Merged bug fix from Stable into Unstable Mark DePristo 2013-03-18 12:36:21 -0400
  • 7ab7c873a1 Temp. to PairHMM to avoid bad likelihoods Mark DePristo 2013-03-18 12:34:51 -0400
  • a67d8c8dd6 Bump timeout for MaxRuntimeIntegrationTest David Roazen 2013-03-17 16:17:29 -0400
  • a67aae0261 Merge pull request #114 from broadinstitute/dr_tweak_test_timeouts droazen 2013-03-15 15:43:55 -0700
  • d86a1242d1 Merge pull request #115 from broadinstitute/md_kb_unstable_server_GSA-778 Mark DePristo 2013-03-15 13:34:10 -0700
  • 2f27e5682a NA12878 KB startup script takes full path to GATK.jar Mark DePristo 2013-03-15 16:33:29 -0400
  • 236eb54abd Trivial script to publish private unstable jars for group use David Roazen 2013-03-15 16:00:59 -0400
  • 090db06793 Merge pull request #110 from broadinstitute/rp_fix_extending_partial_haplotype_bug_GSA-840 Mark DePristo 2013-03-15 11:53:31 -0700
  • 742a7651e9 Further tweaking of test timeouts David Roazen 2013-03-15 12:25:21 -0400
  • e681df68c9 Merge pull request #113 from broadinstitute/dr_parallel_tests_print_exited_classes droazen 2013-03-15 11:41:40 -0700
  • 68c6ebd93f parallel tests: print names of test classes that had an error in real time David Roazen 2013-03-15 14:28:20 -0400
  • 0cf5d30dac Bug fix in assembly for edge case in which the extendPartialHaplotype function was filling in deletions in the middle of haplotypes. Ryan Poplin 2013-03-13 15:51:01 -0400
  • 9d6d1f94b0 Merge pull request #112 from broadinstitute/dr_parallel_tests_print_unfinished_classes droazen 2013-03-15 10:57:59 -0700
  • 4a042e9bff Merge pull request #111 from broadinstitute/rp_no_ref_padding_bug_GSA-860 Mark DePristo 2013-03-15 10:34:45 -0700
  • f42a52c090 parallel tests: start printing the names of unfinished test classes once there are < 10 jobs left David Roazen 2013-03-15 13:08:34 -0400
  • b8991f5e98 Fix for edge case bug of trying to create insertions/deletions on the edge of contigs. Ryan Poplin 2013-03-15 12:31:54 -0400
  • 0fd40dbde9 parallel tests: use experimental Class A storage David Roazen 2013-03-15 10:19:54 -0400
  • daa0f8b551 Merge pull request #109 from broadinstitute/md_qd_fix_for_high_depth Ryan Poplin 2013-03-15 07:05:32 -0700
  • 8317cc155e Merge pull request #108 from broadinstitute/eb_bqsr_out_of_bounds_fix Mark DePristo 2013-03-14 17:29:35 -0700
  • 6f0269df2c Merge pull request #107 from broadinstitute/eb_fix_bqsr_clip_exception MauricioCarneiro 2013-03-14 14:40:06 -0700
  • 232afdcbea Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*'). Eric Banks 2013-03-14 15:30:37 -0400
  • 2d35065238 QualityByDepth remaps QD values > 40 to a gaussian around 30 Mark DePristo 2013-03-06 13:44:48 -0500
  • 0fd9f0e77c Merge pull request #104 from broadinstitute/eb_fix_output_annotation_GSA-837 droazen 2013-03-14 12:52:00 -0700
  • c3b5f66386 run_parallel_tests: further attempts to work around git issues in bamboo David Roazen 2013-03-14 14:49:39 -0400
  • 5d6faef50e Merge pull request #106 from broadinstitute/rp_unknown_sites_assess_as_tp_in_kb Mark DePristo 2013-03-14 11:50:12 -0700
  • 38914384d1 Changing CALLED_IN_DB_UNKNOWN_STATUS to count as TRUE_POSITIVEs in the simplified stats for AssessNA12878. Ryan Poplin 2013-03-12 15:41:28 -0400
  • 6d6264b108 Merge pull request #105 from broadinstitute/gg_annotations_cleanup_45802765 Eric Banks 2013-03-14 11:35:00 -0700
  • ec43112d28 Merge pull request #100 from broadinstitute/eb_maxIndelSize_SV_fix delangel 2013-03-14 11:32:56 -0700
  • 61349ecefa Cleaned up annotations Geraldine Van der Auwera 2013-03-12 16:32:59 -0400
  • 7cab709a88 Fixed the logic of the @Output annotation and its interaction with 'required'. Eric Banks 2013-03-13 14:57:28 -0400
  • 573ed07ad0 Fixed reported bug in BQSR for RNA seq alignments with Ns. Eric Banks 2013-03-14 11:06:45 -0400
  • acaa96f853 parallel_tests: use a safer method to copy the working dir into an LSF-accessible location David Roazen 2013-03-14 11:23:56 -0400
  • be729410b9 run_parallel_tests: use independent java.io.tmpdir for each run David Roazen 2013-03-14 08:02:42 -0400
  • ff87b62fe3 Fixed bug in SelectVariants where maxIndelSize argument wasn't getting applied to deletions. Eric Banks 2013-03-12 13:58:20 -0400
  • 3b4dca1b94 Merge pull request #103 from broadinstitute/md_fragutils Ryan Poplin 2013-03-13 10:12:40 -0700
  • b5b63eaac7 New GATKSAMRecord concept of a strandless read, update to FS Mark DePristo 2013-03-11 14:54:20 -0400
  • 925846c65f Cleanup of FragmentUtils Mark DePristo 2013-02-10 19:21:26 -0800
  • 8ed78b453f Increase timeout for a test in the EngineFeaturesIntegrationTest David Roazen 2013-03-12 23:53:26 -0400