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  • 1143c12c44 Merge pull request #254 from broadinstitute/md_bad_merge MauricioCarneiro 2013-05-31 13:53:14 -0700
  • 6555361742 Fix error in merging code in HC Mark DePristo 2013-05-31 15:21:12 -0400
  • 749f53d60e Merge pull request #253 from broadinstitute/md_bad_compress MauricioCarneiro 2013-05-31 12:40:01 -0700
  • 4b206a3540 Check that -compress arguments are within range 0-9 Mark DePristo 2013-05-31 13:54:33 -0400
  • 64b4d80729 Make BQSR calculateIsIndel robust to indel CIGARs are start/end of read Mark DePristo 2013-05-31 13:16:00 -0400
  • a96f48bc39 Merge pull request #249 from broadinstitute/rp_hc_gga_mode Eric Banks 2013-05-31 10:54:50 -0700
  • a665d759cd Merge pull request #251 from broadinstitute/md_mapq_reassign droazen 2013-05-31 09:05:24 -0700
  • ed4f19d79b Restore scala compilation by default in build.xml David Roazen 2013-05-31 11:28:29 -0400
  • b5b9d745a7 New implementation of the GGA mode in the HaplotypeCaller Ryan Poplin 2013-05-22 10:35:19 -0400
  • 50b4c130ca Merge pull request #250 from broadinstitute/chartl_mathutils_checks_for_valid_inputs-GSA-767 Eric Banks 2013-05-30 21:58:33 -0700
  • 199476eae1 Three squashed commits: Chris Hartl 2013-05-30 22:48:37 -0400
  • b16de45ce4 Command-line read filters are now applied before Walker default filters Mark DePristo 2013-05-30 16:53:23 -0400
  • ac90e6765e Merge pull request #248 from broadinstitute/rp_chartl_mathutils_checks_for_valid_inputs-GSA-767 Mark DePristo 2013-05-30 13:39:33 -0700
  • 61af37d0d2 Create a new normalDistributionLog10 function that is unit tested for use in the VQSR. Ryan Poplin 2013-05-29 16:17:43 -0400
  • 56b14be4bc Merge pull request #247 from broadinstitute/eb_fix_RR_negative_header_problem Mark DePristo 2013-05-29 18:10:19 -0700
  • 50a12df68c Merge pull request #246 from broadinstitute/dr_fix_read_shard_balancer_log_output Mark DePristo 2013-05-29 13:50:26 -0700
  • a5a68c09fa Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads. Eric Banks 2013-05-29 14:42:15 -0400
  • eb206e9f71 Fix confusing log output from the engine David Roazen 2013-05-29 14:43:57 -0400
  • 684c91c2e7 Merge pull request #245 from broadinstitute/dr_enforce_min_dcov Mark DePristo 2013-05-29 09:52:13 -0700
  • 60c3c83b94 Merge pull request #244 from broadinstitute/mc_add_missing_example_vcf_idx Mark DePristo 2013-05-29 09:48:24 -0700
  • 677e6bd6cf Merge pull request #243 from broadinstitute/mc_turn_off_downsampling_in_diagnose_targets Mark DePristo 2013-05-29 09:48:08 -0700
  • a7cb599945 Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage David Roazen 2013-05-28 16:52:28 -0400
  • 38e765f00d Somehow the index of exampleDBSNP.vcf was missing Mauricio Carneiro 2013-05-28 15:29:43 -0400
  • f1affa9fbb Turn off downsampling for DiagnoseTargets Mauricio Carneiro 2013-05-28 14:58:50 -0400
  • 3516daff52 Merge pull request #240 from broadinstitute/rp_gga_implies_both_models Ryan Poplin 2013-05-24 11:13:57 -0700
  • 85905dba92 Bugfix for GGA mode in UG silently ignoring indels Ryan Poplin 2013-05-23 15:15:56 -0400
  • b7fab31e25 Merge pull request #239 from broadinstitute/mc_quick_dt_output_fix Mark DePristo 2013-05-23 07:00:57 -0700
  • da21924b44 Make the missing targets output never use stdout Mauricio Carneiro 2013-05-22 14:22:54 -0400
  • 32c33901d7 Merge pull request #237 from broadinstitute/md_banded_pairhmm MauricioCarneiro 2013-05-22 10:25:18 -0700
  • d167743852 Archived banded logless PairHMM Mark DePristo 2013-05-10 11:09:53 -0400
  • 925232b0fc Merge pull request #236 from broadinstitute/md_simple_hc_performance_improvements delangel 2013-05-22 07:58:28 -0700
  • adec22e748 Merge pull request #238 from broadinstitute/eb_optimize_filter_counting Mark DePristo 2013-05-22 04:57:26 -0700
  • 881b2b50ab Optimized counting of filtered records by filter. Eric Banks 2013-05-21 18:19:23 -0400
  • 010034a650 Optimization/bugfix for PerReadAlleleLikelihoodMap Mark DePristo 2013-05-21 16:01:57 -0400
  • a1093ad230 Optimization for ActiveRegion.removeAll Mark DePristo 2013-05-21 15:35:43 -0400
  • d9cdc5d006 Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet Mark DePristo 2013-05-21 15:32:24 -0400
  • 3cfe2dcc64 Merge pull request #235 from broadinstitute/eb_several_traversal_printout_fixes Mark DePristo 2013-05-21 13:13:11 -0700
  • 20c7a89030 Fixes to get accurate read counts for Read traversals Eric Banks 2013-05-07 13:53:43 -0400
  • 58f4b81222 Count Reads should use a Long instead of an Integer for counts to prevent overflows. Added unit test. Eric Banks 2013-05-07 12:23:24 -0400
  • 1f3624d204 Base Recalibrator doesn't recalibrate all reads, so the final output line was confusing Eric Banks 2013-05-07 11:59:18 -0400
  • 7252238271 Merge pull request #234 from broadinstitute/md_update_gatkperformance_over_time Mark DePristo 2013-05-21 06:14:07 -0700
  • e3d6443d3e Use GATK 2.3 and 2.5 in GATKPerformanceOverTime Mark DePristo 2013-05-21 09:13:16 -0400
  • 71bbb25c9e Merge pull request #231 from broadinstitute/md_combinevariants_bugfix Valentin Ruano Rubio 2013-05-20 14:28:20 -0700
  • 62fc88f92e CombineVariants no longer adds PASS to unfiltered records Mark DePristo 2013-05-20 13:36:30 -0400
  • 2d20e38149 Merge pull request #232 from broadinstitute/rp_hc_gga_mode_active_region_extension Mark DePristo 2013-05-20 12:22:08 -0700
  • 507853c583 Active region boundary parameters need to be bigger when running in GGA mode. CGL performance is quite a bit better as a result. Ryan Poplin 2013-05-20 13:45:01 -0400
  • b239cb76d4 Merge pull request #230 from broadinstitute/mc_gsalib_toR3 Mark DePristo 2013-05-19 04:32:58 -0700
  • c8b1c47764 Updating gsalib for R-3.0 compatibility Mauricio Carneiro 2013-05-18 11:01:06 -0400
  • 665e45f0fc Merge pull request #229 from broadinstitute/eb_liftover_variants_output_required Eric Banks 2013-05-17 07:49:55 -0700
  • 8a442d3c9f @Output needs to be required for LiftoverVariants to prevent a NPE and documentation needed updating. Eric Banks 2013-05-17 09:38:55 -0400
  • 195f0c3e98 Disable CnyPairHMM sathibault 2013-05-17 08:30:23 -0500
  • 92072e1815 Merge pull request #224 from broadinstitute/yf_emit_insert_length_with_pileup MauricioCarneiro 2013-05-16 11:30:19 -0700
  • 3e2a0b15ed - Added a @Hidden option ( -outputInsertLength ) to PileupWalker that causes it to emit insert sizes together with the pileup (to assist Mark Daly's investigation of the contamination dependance on insert length) - Converted my old GATKBAMIndexText (within PileupWalkerIntegrationTest) to use a dataProvider - Added two integration tests to test -outputInsertLength option Yossi Farjoun 2013-05-13 17:19:40 -0400
  • 9234a0efcd Merge pull request #223 from broadinstitute/mc_dt_gaddy_outputs Yossi Farjoun 2013-05-16 09:25:54 -0700
  • a733a5e9b7 Merge pull request #228 from broadinstitute/mc_fine_grained_maxruntime droazen 2013-05-15 05:25:43 -0700
  • 371f3752c1 Subshard timeouts in the GATK Mark DePristo 2013-05-14 17:03:36 -0400
  • 6137e5f89b Merge pull request #227 from broadinstitute/chartl_genotypeconcordance_integration_md5_fix chartl 2013-05-14 17:26:24 -0700
  • 43e78286a0 Merge pull request #226 from broadinstitute/hc_ceu_trio_calling Mark DePristo 2013-05-14 17:02:52 -0700
  • 6da0aed30f Update GCIT md5s to account for trivial changes to description strings Chris Hartl 2013-05-14 19:45:30 -0400
  • 409a202492 Merge pull request #214 from broadinstitute/chartl_genotype_concordance_diploid_and_OGC Yossi Farjoun 2013-05-14 14:19:54 -0700
  • 7d78a77f17 Trivial update to ceutrio.ped file to make it really the CEU trio sample names Mark DePristo 2013-04-14 18:45:27 -0400
  • e9427d817f Merge pull request #225 from broadinstitute/eb_change_consensus_logic_in_kb Mark DePristo 2013-05-14 11:49:43 -0700
  • b951ab1337 Fixed the logic of FP and DISCORDANT consensus. Eric Banks 2013-05-14 12:13:33 -0400
  • de54223aed Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-05-14 10:15:21 -0400
  • 349521e4c2 Merge pull request #220 from broadinstitute/md_nano_hc Mark DePristo 2013-05-13 09:07:13 -0700
  • adcbf947bf Update MD5s and the Diagnose Target scala script Mauricio Carneiro 2013-05-13 11:28:44 -0400
  • 9eceae793a Tool to manipulate intervals outside the GATK Mauricio Carneiro 2013-05-02 13:41:25 -0400
  • 3dbb86b052 Outputting missing intervals in DiagnoseTargets Mauricio Carneiro 2013-04-26 23:29:25 -0400
  • 1466396a31 Diagnose target is outputting intervals out of order Mauricio Carneiro 2013-04-25 01:18:40 -0400
  • 39e4396de0 New ActiveRegionShardBalancer allows efficient NanoScheduling Mark DePristo 2013-05-09 11:39:19 -0400
  • b4f482a421 NanoScheduled ActiveRegionTraversal and HaplotypeCaller Mark DePristo 2013-04-15 08:20:28 -0400
  • 82e6a77385 Merge pull request #221 from broadinstitute/eb_greedy_SW_v2_GSA-936 Mark DePristo 2013-05-13 07:50:50 -0700
  • 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. Eric Banks 2013-05-01 11:13:58 -0400
  • cb49b8cc71 Merge pull request #222 from broadinstitute/dr_convenient_diff_engine_md5_display_in_bamboo_GSA-915 Mark DePristo 2013-05-11 10:58:42 -0700
  • 639030bd6d Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements David Roazen 2013-05-10 17:26:07 -0400
  • 111e8cef0f Merge pull request #219 from broadinstitute/eb_rr_multisample_fix Mark DePristo 2013-05-09 15:31:14 -0700
  • 1078d0e51c Merge pull request #216 from broadinstitute/md_better_assembly Ryan Poplin 2013-05-09 07:36:17 -0700
  • 8b9c6aae3e Fix bug in Reduce Reads that arises in multi-sample mode. Eric Banks 2013-05-08 23:23:51 -0400
  • fa8a47ceef Replace DeBruijnAssembler with ReadThreadingAssembler Mark DePristo 2013-04-18 08:17:15 -0400
  • d3c9910af6 Cosmetic changes (comments and variable names) to GenotypeConcordance and ConcordanceMetrics to address reviewer comments. Chris Hartl 2013-05-08 17:25:14 -0400
  • d79b5f0931 Adding Convey HC-1 HMM acceleration sathibault 2013-05-08 11:01:20 -0500
  • fbc683f1e8 Merge pull request #218 from broadinstitute/dr_rev_picard_to_1.91 Mark DePristo 2013-05-07 14:32:03 -0700
  • 52c20a8416 Rev picard, sam-jdk, tribble, and variant to version 1.91.1453 David Roazen 2013-05-07 14:21:15 -0400
  • 178f1499ee Merge pull request #217 from broadinstitute/md_queue_jobreport_improvements Mark DePristo 2013-05-07 09:14:03 -0700
  • 2b86ab02be Improve queue script jobreport visualization script Mark DePristo 2013-05-07 12:11:46 -0400
  • b153042a9d Merge pull request #215 from broadinstitute/eb_misc_improvements Mark DePristo 2013-05-07 06:05:53 -0700
  • d242f1bba3 Secondary alignments were not handled correctly in IndelRealigner Eric Banks 2013-05-06 19:00:58 -0400
  • b53336c2d0 Added hidden mode for BQSR to force all read groups to be the same one. Eric Banks 2013-05-06 14:57:01 -0400
  • c7dcc2b53b Fix to deal with multi-generational families being allowed if only one level (one 'trio', effectively) appears in the VCF Menachem Fromer 2013-05-06 15:47:27 -0400
  • 86287dce76 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-05-06 13:52:55 -0400
  • 13240588cf Fix to only consider the samples that are both in the PED file and in the VCF file Menachem Fromer 2013-05-06 13:52:14 -0400
  • 09995b6900 Use GenomeLocParse in a non-deprecated way Menachem Fromer 2013-05-06 13:50:57 -0400
  • 6ff74deac7 Add overall genotype concordance to the genotype concordance tool. In addition, protect from non-diploid genotypes, which can cause very strange behavior. Update MD5 sums. As expected, md5 changes are consistent with the genotype concordance field being added to each output. Chris Hartl 2013-05-06 12:11:04 -0400
  • 98021db264 Merge pull request #208 from broadinstitute/yf_fix_molten_GenotypeConcordance chartl 2013-05-06 08:42:06 -0700
  • 78e958bf39 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-05-06 10:39:21 -0400
  • 084a464779 Merge pull request #213 from broadinstitute/gda_md5_fix Mark DePristo 2013-05-03 16:21:46 -0700
  • 874dc8f9c1 Re-fix md5's that changed due to conflicting pushes Guillermo del Angel 2013-05-03 14:59:16 -0400
  • 8bac61f9fb Merge pull request #212 from broadinstitute/md_misc_improvements Mark DePristo 2013-05-03 08:20:55 -0700
  • f42bb86bdd e# This is a combination of 2 commits. Mark DePristo 2013-04-24 16:01:43 -0400
  • 0587a145bf Utils.dupString should allow 0 number of duplicates to produce empty string Mark DePristo 2013-04-23 18:28:41 -0400