zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Commit Graph

  • 711cbd3b5a Archiving CoverageBySample Mauricio Carneiro 2013-02-26 13:49:00 -0500
  • 357a05683d Merge pull request #65 from broadinstitute/dr_change_haplotypecaller_downsampling_settings_GSA-699 Ryan Poplin 2013-02-26 10:33:19 -0800
  • 8b29030467 Change default downsampling coverage target for the HaplotypeCaller to 250 David Roazen 2013-02-25 15:38:29 -0500
  • 51d618de97 Merge pull request #62 from broadinstitute/rp_increase_max_kmer_in_assembly depristo 2013-02-26 05:37:02 -0800
  • 79d1050457 AGBT analysis scripts Mark DePristo 2013-02-19 08:29:40 -0500
  • ed5aff3702 Merge pull request #55 from broadinstitute/dr_fix_sequence_dictionary_validation_GSA-768 depristo 2013-02-25 12:39:56 -0800
  • 396b7e0933 Fixed the intermittent PairHMM unit test failure. Eric Banks 2013-02-25 14:58:17 -0500
  • 7519484a38 Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods. Eric Banks 2013-02-25 12:24:35 -0500
  • 89e2943dd1 The maximum kmer length is derived from the reads. Ryan Poplin 2013-02-25 14:00:38 -0500
  • bd9875aff5 Merge pull request #61 from broadinstitute/dr_update_release_scripts MauricioCarneiro 2013-02-25 10:37:59 -0800
  • 0ff3343282 Addressing Eric's comments Mauricio Carneiro 2013-02-25 13:33:47 -0500
  • 3645ea9bb6 Sequence dictionary validation: detect problematic contig indexing differences David Roazen 2013-02-21 15:31:16 -0500
  • baa3b15207 Update release scripts in preparation for open-sourcing protected David Roazen 2013-02-25 10:17:16 -0500
  • f62dd84869 Merge pull request #57 from broadinstitute/rp_bubble_traversal_merge_GSA-680 Eric Banks 2013-02-24 05:08:05 -0800
  • 9e5a31b595 Brought all of ReduceReads to fastutils Mauricio Carneiro 2013-02-23 17:32:19 -0500
  • 6a639c8ffc Replace Smith-Waterman alignment with the bubble traversal. Ryan Poplin 2013-02-05 17:12:53 -0500
  • 2ad559cf58 Merge pull request #59 from broadinstitute/mc_reving_testng_GSA-695 depristo 2013-02-22 10:39:04 -0800
  • 50612ac981 Merge pull request #58 from broadinstitute/mc_callset_assesment_GSATDG-52 depristo 2013-02-22 07:23:59 -0800
  • 3f901ff0e7 R scripts for covreage analysis of the genome (AGBT13) Mauricio Carneiro 2013-02-21 20:11:16 -0500
  • e3f01673e1 Implementation of the find and diagnose Queue script Mauricio Carneiro 2013-02-19 21:07:36 -0500
  • 15a8f6d82e Coverage analysis by variant type R script (for AGBT13) Mauricio Carneiro 2013-02-21 12:09:18 -0500
  • a0b1e15dd0 Coverage distribution R script Mauricio Carneiro 2013-02-16 17:09:07 -0500
  • 8ae2e7be4f Queue scripts to process call and assess callsets (for AGBT13) Mauricio Carneiro 2013-02-13 15:02:32 -0500
  • 1690be0866 Adding functionality to NA12878KB walkers Mauricio Carneiro 2013-02-08 19:28:10 -0500
  • 34ee953798 Merge pull request #56 from broadinstitute/md_relax_boundquals_checks Eric Banks 2013-02-22 07:08:41 -0800
  • 4ac50c89ad Updating TestNG to the latest version Mauricio Carneiro 2013-02-14 22:02:30 -0500
  • c8a01e6569 Merge pull request #53 from broadinstitute/rp_pcrfree_bad_mappingquality_GSA-780 depristo 2013-02-22 05:52:50 -0800
  • 182c32a2b7 Relax bounds checking in QualityUtils.boundQual Mark DePristo 2013-02-21 18:18:10 -0500
  • 48c699eec6 Merge pull request #54 from broadinstitute/md_improve_kb Eric Banks 2013-02-22 05:20:06 -0800
  • 8ac6d3521f Vast improvements to AssessNA12878 code and functionality Mark DePristo 2013-02-19 20:19:49 -0500
  • 62e14f5b58 Bug fix in LikelihoodCalculationEngine: Mapping quality was being cast to a byte and overflowing for reads with large mapping quality scores. Ryan Poplin 2013-02-21 12:53:13 -0500
  • 29319bf222 Improved allele trimming code in GATKVariantContextUtils Mark DePristo 2013-02-19 17:20:26 -0500
  • f714ecc0ae Cleanup and improvements to NA12878 KB consensus creation Mark DePristo 2013-02-18 16:28:10 -0500
  • 09b444de26 Merge pull request #51 from broadinstitute/eb_optimize_hc_haplotype_comparisons depristo 2013-02-21 07:16:28 -0800
  • 6996a953a8 Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample). Eric Banks 2013-02-20 13:52:55 -0500
  • a954cf3c01 Merge pull request #52 from broadinstitute/gg_more_gatkdocs_improvements_GSATDG-66-67 MauricioCarneiro 2013-02-21 06:48:35 -0800
  • c3e01fea40 Added several more info types / annotations to GATKDocs -- top-level walker type (locus, read etc) -- parallelism options (nt or nct) -- annotation type (for Variant Annotations) -- downsampling settings that override engine defaults -- reference window size -- active region settings -- partitionBy info Geraldine Van der Auwera 2013-02-20 15:13:51 -0500
  • 0c34e47a87 Merge pull request #50 from broadinstitute/gg_new_ReassignOneMappingQualityFilter_GSATDG-77 Eric Banks 2013-02-20 04:51:45 -0800
  • 551d33686c Merge pull request #47 from broadinstitute/aw_reduceread_perf_1_GSA-761 Eric Banks 2013-02-20 04:49:07 -0800
  • e674b4a524 Added new ReadFilter that allows users to specifically reassign one single mapping quality to a different value. Useful for TopHat and other RNA-seq software users. Geraldine Van der Auwera 2013-02-19 16:53:14 -0500
  • 76810465aa Merge pull request #40 from broadinstitute/gg_retrieve_readfilters_GSATDG-63 MauricioCarneiro 2013-02-19 19:42:35 -0800
  • 910d966428 Extend timeout of NanoScheduler deadlock tests Mark DePristo 2013-02-19 20:25:25 -0500
  • 9dfdb9528b Merge pull request #49 from broadinstitute/gda_hidden_ug_args Eric Banks 2013-02-19 16:18:32 -0800
  • 0055a6f1cd Merge pull request #45 from broadinstitute/mc_fix_indelrealigner_GSA-774 Eric Banks 2013-02-19 16:16:48 -0800
  • 5a0a9bc488 Hide arguments related to reference sample operation in UG - for internal use only until paper is published and docs are polished. Guillermo del Angel 2013-02-19 10:18:35 -0500
  • 334d124145 Merge pull request #48 from broadinstitute/rp_calcAlignmentByteArrayOffset_contract_GSA-772 depristo 2013-02-19 15:09:58 -0800
  • faef85841b Added GATKDocs fct to indicate default Read Filters for each tool Geraldine Van der Auwera 2013-02-13 01:14:57 -0500
  • 371ea2f24c Fixed IndelRealigner reference length bug (GSA-774) Mauricio Carneiro 2013-02-16 20:37:41 -0500
  • 815028edd4 Added verbose error message to the PluginManager Mauricio Carneiro 2013-02-18 11:11:18 -0500
  • ab75e053da Reduce memory footprint of SyntheticRead by replacing several Lists with a single List of a small private static class that contains the attributes that were scattered across the several Lists. Alec Wysoker 2013-02-19 11:29:07 -0500
  • c025e84c8b Fix for calculating read pos rank sum test with reads that are informative but don't actually overlap the variant due to some hard clipping. Ryan Poplin 2013-02-15 14:46:56 -0500
  • 8eda0c50df Merge pull request #46 from broadinstitute/md_active_regions_GSA-770 Eric Banks 2013-02-19 09:49:47 -0800
  • be45edeff2 ActivityProfile and ActiveRegions respects engine interval boundaries Mark DePristo 2013-02-14 09:36:06 -0800
  • e919d62156 Merge pull request #44 from broadinstitute/rp_hc_reference_padding MauricioCarneiro 2013-02-17 21:46:58 -0800
  • b7e9c342c7 Reducing the size of the reference padding in the HaplotypeCaller. Ryan Poplin 2013-02-17 11:09:00 -0500
  • 029de71a44 Merge pull request #43 from broadinstitute/md_qualutils_cleanup MauricioCarneiro 2013-02-16 12:59:26 -0800
  • 73a363b166 Update MD5s due to new QualityUtils calculations Mark DePristo 2013-02-11 13:47:31 -0800
  • 3b67aa8aee Final edge case bug fixes to QualityUtil routines Mark DePristo 2013-02-11 12:42:50 -0800
  • b393c27f07 QualityUtils now uses runtime argument checks instead of contract Mark DePristo 2013-02-11 11:03:15 -0800
  • 3231031c1a Bugfix for FisherStrand Mark DePristo 2013-02-11 11:16:19 -0800
  • 9a29d6d4be Fix an catastrophic bug (WoW!) in the reference calculation of the UG Mark DePristo 2013-02-11 10:42:37 -0800
  • 9e28d1e347 Cleanup and unit tests for QualityUtils Mark DePristo 2013-02-09 13:04:30 -0500
  • 307f709cc7 Merge pull request #42 from broadinstitute/yf_add_version_information_CL_option MauricioCarneiro 2013-02-15 21:39:33 -0800
  • aa99a5f47c Added an option to print out the version string Yossi Farjoun 2013-02-15 12:38:29 -0500
  • bbfbe1bc26 Merge pull request #41 from broadinstitute/jt_cmi_queue_packaging MauricioCarneiro 2013-02-15 09:19:00 -0800
  • 664960373d Merge pull request #31 from broadinstitute/yf_fast_BAM_index_traversal droazen 2013-02-15 09:12:32 -0800
  • 182a950202 ValidatingPileup was renamed to CheckPileup Joel Thibault 2013-02-15 11:55:28 -0500
  • d80b99143f Merge pull request #37 from broadinstitute/rp_left_alignment_hc_contract_GSA-771 MauricioCarneiro 2013-02-15 08:32:45 -0800
  • 1dd284a5bb Merge pull request #39 from broadinstitute/tj_printreads_tag_for_bqsr_GSA-720 MauricioCarneiro 2013-02-15 07:18:28 -0800
  • b58a0eca6b Merge pull request #33 from broadinstitute/gg_more_gatkdocs_tweaks_GSATDG-62 MauricioCarneiro 2013-02-14 22:35:07 -0800
  • f2669c8438 Merge pull request #38 from broadinstitute/gda_hc_md5 MauricioCarneiro 2013-02-14 22:19:23 -0800
  • 6cb80591e3 PrintReads writes a header when used with -BQSR Tad Jordan 2013-02-13 13:45:49 -0500
  • b18f216033 Updated md5's from BiasedDownsamplerIntegrationTest that changed due to changes in HaplotypeCaller - changing HashMaps to LinkedHashMaps changed ordering of reads presented to BiasedDownSampler which changed reads chosen, thereby marginally changing PL's and some site info. Guillermo del Angel 2013-02-14 20:18:49 -0500
  • 3a7c8c13e2 Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream This helps a lot since FileChannel is very low-level and traversing the BAMIndex involves lots of short reads. Yossi Farjoun 2013-02-01 15:46:14 -0500
  • 871c8b3866 No need to consider haplotypes which Smith-Waterman aligns off the end of the large padded reference. Ryan Poplin 2013-02-14 11:18:10 -0500
  • 5cc5aedcd1 Merge pull request #34 from broadinstitute/md_longer_default_timeout depristo 2013-02-13 17:44:30 -0800
  • f92328a1a1 Extend default timeout to 20 minutes Mark DePristo 2013-02-13 17:43:30 -0800
  • 6208742f7c Refactored GATKDocs categories some more ( GSATDG-62 ) Geraldine Van der Auwera 2013-02-12 16:27:18 -0500
  • 357d196dad Merge pull request #32 from broadinstitute/yf_per-sample-downsampling_GSA_765 depristo 2013-02-13 10:08:11 -0800
  • 6d12e5a54f Fixed md5s for the per-sample downsampling IntegrationTests that were disabled. - got md5s from a interim version that does not have the per-sample downsampling hookedup - added an integration test that forces the result from flat-downsampling to equal that which results from an equivalent flat contamination file Yossi Farjoun 2013-02-05 18:06:13 -0500
  • 961f2533a5 Merge pull request #29 from broadinstitute/gda_gga_hc_GSA-722 depristo 2013-02-13 07:58:57 -0800
  • 4308b27f8c Fixed non-determinism in HaplotypeCaller and some UG calls - Guillermo del Angel 2013-02-11 14:59:46 -0500
  • 38cea0a7ab Merge pull request #28 from broadinstitute/gg_reorganize_gatkdocs_categories_GSATDG-62 depristo 2013-02-12 11:11:45 -0800
  • dff5ef562b Reorganized walker categories in GATKDocs (@DocumentedGATKFeature details) Geraldine Van der Auwera 2013-02-12 12:48:20 -0500
  • 59484dfae4 Merge pull request #27 from broadinstitute/rp_ranksumtest_optimization depristo 2013-02-11 08:58:22 -0800
  • 3f2f837b6a Optimization to ReadPosRankSumTest: Don't do the work of parsing through the cigar string for non-informative reads. Ryan Poplin 2013-02-11 11:29:42 -0500
  • f8e2153c71 Merge pull request #25 from broadinstitute/md_hmm_fail_GSA-751 delangel 2013-02-09 16:43:50 -0800
  • b4417dff5b Updating MD5s due to changes in HMM Mark DePristo 2013-02-09 10:00:13 -0500
  • 35139cf990 HaplotypeScore only annotates SNPs Mark DePristo 2013-02-08 15:13:34 -0500
  • e40d83f00e Final version of PairHMMs with correct edge conditions Mark DePristo 2013-02-06 22:14:23 -0500
  • 09595cdeb9 Remove ExactPairHMM and OriginalPairHMM, everyone just uses Log10PairHMM with appropriate arguments Mark DePristo 2013-02-06 21:15:31 -0500
  • 2d802e17a4 Delete the CachingPairHMM Mark DePristo 2013-02-06 21:05:33 -0500
  • 7dcafe8b81 Preliminary version of LoglessCachingPairHMM that avoids positive likelihoods Mark DePristo 2013-02-06 17:27:12 -0500
  • b7593aeadc Removing the symlink from the private license file Mauricio Carneiro 2013-02-09 12:57:44 -0500
  • ca76de0619 Move ProcessUtilsUnitTest to private Mark DePristo 2013-02-09 12:34:45 -0500
  • f5e52b72ea Merge pull request #23 from broadinstitute/md_process_utils_unit_tests MauricioCarneiro 2013-02-09 09:27:31 -0800
  • 3ff10ab277 Merge pull request #24 from broadinstitute/md_ngsplatform_unittests MauricioCarneiro 2013-02-09 09:27:03 -0800
  • 7dbdc4ea6a Merge pull request #22 from broadinstitute/md_better_contig_comparer MauricioCarneiro 2013-02-09 09:26:37 -0800
  • b127fc6a1a Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests Mark DePristo 2013-02-09 11:16:21 -0500
  • fc3307a97f UnitTests for ProcessUtils Mark DePristo 2013-02-09 10:13:01 -0500