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  • ee51195bf5 Merge pull request #170 from broadinstitute/mc_hmm_mantissa_optimize Mark DePristo 2013-04-15 10:23:56 -0700
  • 9bfa5eb70f Quick optimization to the PairHMM Mauricio Carneiro 2013-04-14 23:25:33 -0400
  • 55547b68bb Merge pull request #169 from broadinstitute/md_ug_bugfix MauricioCarneiro 2013-04-13 12:05:53 -0700
  • 3144eae51c UnifiedGenotyper bugfix: don't create haplotypes with 0 bases Mark DePristo 2013-04-13 14:53:30 -0400
  • 6c9360b020 Merge pull request #167 from broadinstitute/gda_read_adaptor_trimmer_improvements delangel 2013-04-13 10:43:45 -0700
  • a971e7ab6d Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed): -- Add pair cleaning feature. Reads in query-name sorted order are required and pairs need to appear consecutively, but if -cleanPairs option is set, a malformed pair where second read is missing is just skipped instead of erroring out. -- Add integration tests -- Move walker to public Guillermo del Angel 2013-04-08 18:49:05 -0400
  • a5301e17a2 Merge pull request #168 from broadinstitute/mc_update_example_grp Mark DePristo 2013-04-13 08:01:07 -0700
  • a063e79597 Updating the exampleGRP.grp test file Mauricio Carneiro 2013-04-13 09:07:13 -0400
  • f11c8d22d4 Updating java 7 md5's to java 6 md5's Mauricio Carneiro 2013-04-13 08:21:48 -0400
  • 776f5a2f6f Merge pull request #164 from broadinstitute/mc_clia_scripts Mark DePristo 2013-04-12 13:08:18 -0700
  • 09d29e5d0d In HaplotypeCallerScript: * fix downsampling parameter * fix the default value of required fields (_ instead of .) * add support to multiple interval files Mauricio Carneiro 2013-04-11 11:25:51 -0400
  • 802ae76905 Script for coverage evaluation of exomes and targeted sequencing projects in the Genomics Platform Mauricio Carneiro 2013-04-04 11:09:52 -0400
  • b32457be8d Merge pull request #163 from broadinstitute/mc_hmm_caching_again Mark DePristo 2013-04-12 12:34:49 -0700
  • 403f9de122 Fix another caching issue with the PairHMM Mauricio Carneiro 2013-04-12 10:42:03 -0400
  • e5b9b6041c Merge pull request #162 from broadinstitute/md_path_sw_update Ryan Poplin 2013-04-12 10:38:26 -0700
  • 0e627bce93 Slight update to Path SW parameters. Mark DePristo 2013-04-12 12:42:47 -0400
  • 4ef6e0deb1 Merge pull request #161 from broadinstitute/md_unstable_sw Ryan Poplin 2013-04-12 07:59:43 -0700
  • 50cdffc61f Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons Mark DePristo 2013-04-10 10:54:25 -0400
  • 74196ff7db Trivial BQSR bug fixes and improvement Mark DePristo 2013-04-11 15:35:09 -0400
  • 35293cde49 Merge pull request #160 from broadinstitute/rp_bqsr_gatherer_works_with_empty_tables Mark DePristo 2013-04-11 14:07:24 -0700
  • a507381a33 Updating BQSR RecalibrationEngine to work correctly with empty BQSR tables. Ryan Poplin 2013-04-11 15:05:19 -0400
  • 44230b97eb Merge pull request #158 from broadinstitute/hc_fast_kmer_graph_creation delangel 2013-04-11 12:09:01 -0700
  • fb86887bf2 Fast algorithm for determining which kmers are good in a read Mark DePristo 2013-04-08 17:19:08 -0400
  • bf42be44fc Fast DeBruijnGraph creation using the kmer counter Mark DePristo 2013-04-08 07:17:53 -0400
  • 7d267639d8 Merge pull request #157 from broadinstitute/rp_smith_waterman_failing_test Mark DePristo 2013-04-10 13:54:25 -0700
  • 850be5e9da Bug fix in SWPairwiseAlignment. Ryan Poplin 2013-04-10 11:23:29 -0400
  • 2fb8b61dd0 Merge pull request #152 from broadinstitute/md_commonsuffix_infinite_loop_bugfix Eric Banks 2013-04-09 17:43:11 -0700
  • 97fd8c5893 Merge pull request #156 from broadinstitute/dr_github_mirror_daemon droazen 2013-04-09 16:56:20 -0700
  • e187258481 Daemon script to continually update local mirrors of our github repositories David Roazen 2013-04-09 16:49:32 -0400
  • b115e5c582 Critical bugfix for CommonSuffixSplitter to avoid infinite loops Mark DePristo 2013-04-08 14:00:51 -0400
  • 0194c9492d Merge pull request #155 from broadinstitute/md_pnrm Mark DePristo 2013-04-09 12:20:55 -0700
  • 51954ae3e5 HaplotypeCaller doesn't support EXACT_GENERAL_PLOIDY model Mark DePristo 2013-04-09 15:18:42 -0400
  • 55c9542bfd Merge pull request #154 from broadinstitute/mc_printreads_presorted Mark DePristo 2013-04-09 11:58:57 -0700
  • b8bd10469d Merge pull request #153 from broadinstitute/md_hc_ld_merge_off Ryan Poplin 2013-04-09 07:12:16 -0700
  • 33ecec535d Turn off the LD merging code by default Mark DePristo 2013-04-09 09:52:56 -0400
  • 3960733c88 Fix PrintReads out of space issue Mauricio Carneiro 2013-04-09 08:19:52 -0400
  • ae0612b6e8 Merge pull request #150 from broadinstitute/md_hc_excessive_coverage droazen 2013-04-08 13:40:39 -0700
  • 1b36db8940 Make ActiveRegionTraversal robust to excessive coverage Mark DePristo 2013-04-07 15:25:52 -0400
  • 317dc4c323 Add size() method to Downsampler interface Mark DePristo 2013-04-07 12:20:44 -0400
  • 0c2f795fa5 Merge pull request #147 from broadinstitute/md_hc_symbolic_allele Ryan Poplin 2013-04-08 10:29:07 -0700
  • 469dc7f22c Update KMerErrorCorrectorUnitTest license text Mark DePristo 2013-04-06 14:41:10 -0400
  • 21410690a2 Address reviewer comments Mark DePristo 2013-04-06 14:08:26 -0400
  • caf15fb727 Update MD5s to reflect new HC algorithms and parameter values Mark DePristo 2013-04-05 14:11:06 -0400
  • 6d22485a4c Critical bugfix to ReduceRead functionality of the GATKSAMRecord Mark DePristo 2013-04-05 13:50:03 -0400
  • 3097936a3d Update GeneralCallingPipeline Mark DePristo 2013-04-01 17:34:07 -0400
  • 5a54a4155a Change key Haplotype default parameter values Mark DePristo 2013-04-04 20:29:17 -0400
  • 3a19266843 Fix residual merge conflicts Mark DePristo 2013-04-04 16:07:00 -0400
  • 9c7a35f73f HaplotypeCaller no longer creates haplotypes that involve cycles in the SeqGraph Mark DePristo 2013-04-04 15:15:10 -0400
  • 5545c629f5 Rename Utils to GraphUtils to avoid conflicts with the sting.Utils class; fix broken unit test in SharedVertexSequenceSplitterUnitTest Mark DePristo 2013-04-04 10:24:12 -0400
  • 15461567d7 HaplotypeCaller no longer uses reads with poor likelihoods w.r.t. any haplotype Mark DePristo 2013-04-03 18:47:59 -0400
  • 9b5c55a84a LikelihoodCalculationEngine will now only use reads longer than the minReadLength, which is currently fixed at 20 bp Mark DePristo 2013-04-03 08:59:09 -0400
  • af593094a2 Major improvements to HC that trims down active regions before genotyping Mark DePristo 2013-03-30 14:22:45 -0400
  • 4d389a8234 Optimizations for HC infrastructure Mark DePristo 2013-03-31 16:57:36 -0400
  • e916998784 Bugfix for head and tail merging code in SeqGraph Mark DePristo 2013-04-03 10:39:45 -0400
  • 2aac9e2782 More efficient ZipLinearChains algorithm Mark DePristo 2013-03-31 14:40:14 -0400
  • 7105ad65a6 Remove the capability of EventMap to emit symbolic alleles for unassembled events Mark DePristo 2013-04-02 15:57:45 -0400
  • f1d772ac25 LD-based merging algorithm for nearby events in the haplotypes Mark DePristo 2013-03-28 18:17:27 -0400
  • 167cd49e71 Added -forceActive argument to ActiveRegionWalkers Mark DePristo 2013-03-28 17:35:00 -0400
  • 8656bd5e29 Haplotype now consolidates cigars in setCigar Mark DePristo 2013-03-28 09:40:08 -0400
  • 67cd407854 The GenotypingEngine now uses the samples from the mapping of Samples -> PerReadAllele likelihoods instead of passing around a redundant list of samples Mark DePristo 2013-03-27 09:41:04 -0400
  • 0310499b65 System to merge multiple nearby alleles into block substitutions Mark DePristo 2013-03-27 09:36:14 -0400
  • bff13bb5c5 Move Haplotype class to its own package in utils Mark DePristo 2013-03-27 08:34:28 -0400
  • b7d59ea13b LIBS unit test debugging should be false Mark DePristo 2013-04-01 10:43:43 -0400
  • 7cd804f97c Merge pull request #149 from broadinstitute/gda_ancient_dna_newPipeline Mark DePristo 2013-04-08 09:32:46 -0700
  • c9d3c67a9b Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity: -- Picard extension so Queue scripts can use FastqToSam -- Single-sample BAM processing: merge/trim reads + BWA + IR + MD + BQSR. Mostly identical to standard pipeline, except for the adaptor trimming/merging which is critical for short-insert libraries. -- Single-sample calling (experimental, work in progress): standard UG run but outputting at all sites, meant for deep whole genomes. Guillermo del Angel 2013-04-08 11:44:22 -0400
  • 4cc4bb36aa Merge pull request #148 from broadinstitute/mc_fix_hmm_caching delangel 2013-04-08 08:09:13 -0700
  • ebe2edbef3 Fix caching indices in the PairHMM Mauricio Carneiro 2013-04-05 09:21:59 -0400
  • 56f4529ef3 Merge pull request #145 from broadinstitute/eb_various_minor_fixes Mark DePristo 2013-04-05 06:06:54 -0700
  • 6253ba164e Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs Eric Banks 2013-04-04 12:02:22 -0500
  • 7897d52f32 Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). Eric Banks 2013-04-04 10:44:40 -0500
  • 14bbba0980 Optimization to method for getting values in ArgumentMatch Eric Banks 2013-04-03 17:37:19 -0500
  • 03811b4274 Merge pull request #146 from broadinstitute/dr_fix_NA12878KBUnitTestBase Mark DePristo 2013-04-04 17:40:48 -0700
  • 2f42aa5d5d NA12878KBUnitTestBase: use @BeforeSuite method instead of unannotated static initializer block David Roazen 2013-04-04 16:03:48 -0400
  • 78f32ee048 Merge pull request #144 from broadinstitute/dr_disable_contracts_for_tests MauricioCarneiro 2013-04-04 09:44:28 -0700
  • 6197078c5d Disable Contracts for Java for tests David Roazen 2013-04-04 11:56:17 -0400
  • 5e622557a7 Merge pull request #142 from broadinstitute/rp_duplicate_active_regions_GSA-912 Mark DePristo 2013-04-03 12:00:26 -0700
  • 8a93bb687b Critical bug fix for the case of duplicate map calls in ActiveRegionWalkers with exome interval lists. Ryan Poplin 2013-04-01 14:28:20 -0400
  • 09edee2c97 Merge pull request #141 from broadinstitute/md_linkedhashsets Mark DePristo 2013-04-02 17:42:07 -0700
  • 95be16dca7 Merge pull request #143 from broadinstitute/dr_disable_auto_fai_dict_creation_GSA-866 droazen 2013-04-02 15:50:47 -0700
  • 2eac97a76c Remove auto-creation of fai/dict files for fasta references David Roazen 2013-04-02 17:04:44 -0400
  • bb42c90f2b Use LinkedHashSets in incoming and outgoing vertex functions in BaseGraph Mark DePristo 2013-04-02 15:31:09 -0400
  • e7a8e6e8ee Merge pull request #140 from broadinstitute/dr_interval_intersection_bug_GSA-909 Mark DePristo 2013-04-02 11:59:01 -0700
  • b4b58a3968 Fix unprintable character in a comment from the BaseEdge class David Roazen 2013-04-02 14:24:23 -0400
  • 5baf906c28 Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists David Roazen 2013-04-01 15:32:40 -0400
  • d412605c9b Merge pull request #139 from broadinstitute/md_bugfix_suffix_splitter Ryan Poplin 2013-04-02 07:11:45 -0700
  • c191d7de8c Critical bugfix for CommonSuffixSplitter Mark DePristo 2013-04-02 09:20:34 -0400
  • a58a3e7e1e Merge pull request #134 from broadinstitute/mc_phmm_experiments Ryan Poplin 2013-04-01 12:10:43 -0700
  • 791c386972 Merge pull request #138 from broadinstitute/rp_hc_gga_alleles_rod_GSA-908 Mark DePristo 2013-04-01 08:28:23 -0700
  • f65206e758 Two changes to HC GGA mode to make it more like the UG. Ryan Poplin 2013-04-01 10:20:04 -0400
  • 7c83efc1b9 Merge pull request #135 from broadinstitute/mc_pgtag_fix Mark DePristo 2013-03-31 11:36:40 -0700
  • 7dd58f671f Merge pull request #132 from broadinstitute/gda_filter_unmasked_sites Eric Banks 2013-03-31 06:27:26 -0700
  • 4f828ca86f Merge pull request #137 from broadinstitute/eb_more_rr_tests Mark DePristo 2013-03-31 05:50:27 -0700
  • 9686e91a51 Added small feature to VariantFiltration to filter sites outside of a given mask: -- Sometimes it's desireable to specify a set of "good" regions and filter out other stuff (like say an alignability mask or a "good regions" mask). But by default, the -mask argument in VF will only filter sites inside a particular mask. New argument -filterNotInMask will reverse default logic and filter outside of a given mask. -- Added integration test, and made sure we also test with a BED rod. Guillermo del Angel 2013-03-25 17:13:40 -0400
  • 8e2094d2af Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests. Eric Banks 2013-03-25 12:02:12 -0400
  • baf5240e2b Merge pull request #136 from broadinstitute/gda_leftalign_fix Eric Banks 2013-03-30 18:23:39 -0700
  • ec475a46b1 Fixing @PG tag uniqueness issue Mauricio Carneiro 2013-03-29 10:10:13 -0400
  • 52e67a6973 ReviewedStingException -> IllegalStateException Mauricio Carneiro 2013-03-30 20:11:55 -0400
  • 68bf470524 making LoglessPairHMM final Mauricio Carneiro 2013-03-30 20:00:45 -0400
  • 6b8bed34d0 Big bad bug fix: feature added to LeftAlignAndTrimVariants to left align multiallelic records didn't work. -- Corrected logic to pick biallelic vc to left align. -- Added integration test to make sure this feature is tested and feature to trim bases is also tested. Guillermo del Angel 2013-03-30 19:05:04 -0400
  • 0de6f55660 PairHMM rework Mauricio Carneiro 2013-03-26 15:42:41 -0400