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  • cbf290ada0 Reving CoverageByRG to the new GATKReport API Mauricio Carneiro 2012-08-15 16:09:51 -0400
  • 9b84fa20bf Fix an issue with the classpath for external builds in build.xml David Roazen 2012-08-15 15:56:54 -0400
  • db92671b7f Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-15 13:32:07 -0400
  • 7599f94296 Updating large-scale validation script to new UG syntax Guillermo del Angel 2012-08-15 13:31:45 -0400
  • 87e41c83c5 In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC. Eric Banks 2012-08-14 15:02:30 -0400
  • 8e3774fb0e Fixing behavior of the --regenotype argument in SelectVariants to properly run in GenotypeGivenAlleles mode. Added integration tests to cover recent SV changes. Eric Banks 2012-08-14 14:21:42 -0400
  • 34b62fa092 Two changes to SelectVariants: 1) don't add DP INFO annotation if DP wasn't used in the input VCF (it was adding DP=0 previously). 2) If MLEAC or MLEAF is present in the original VCF and the number of samples decreases, remove those annotations from the VC. Eric Banks 2012-08-14 12:54:31 -0400
  • cfb994abd2 Trivial removal of ununsed variable (mentioned in resolved JIRA entry) Eric Banks 2012-08-13 22:55:02 -0400
  • f809f24afb Removed SelectHeader's --include_reference_name option since the reference is always included. In SelectHeaders instead of including the path to the file, only include the name of the reference since dbGaP does not like paths in headers. Khalid Shakir 2012-08-13 16:49:27 -0400
  • 22b4466cf5 Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error. Implemented a mixin called "RetryMemoryLimit" which will by default double the memory. GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'. Java optimizations now enabled by default: - Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier). - Exit if GC spends more than 50% of time in GC (thanks ktibbett). - Exit if GC reclaims lest than 10% of max heap (thanks ktibbett). Added a -noGCOpt command line option to disable new java optimizations. Khalid Shakir 2012-08-13 15:37:35 -0400
  • 6ad75d2f5c Reverting changes to BCF2 ranges Mark DePristo 2012-08-13 15:06:28 -0400
  • 4d3fad38e9 Increase allowable range for BCF2 by -1 on low-end Mark DePristo 2012-08-13 14:20:26 -0400
  • 4cbd11faf5 Fixed spelling error in BQSR.R Mark DePristo 2012-08-13 10:01:33 -0400
  • aab417c94d Fix missing argument in unittest Mark DePristo 2012-08-12 13:58:14 -0400
  • f032e0aba4 A bit better output for ContextCovariate context size logging Mark DePristo 2012-08-12 13:45:52 -0400
  • 243af0adb1 Expanded the BQSR reporting script Mark DePristo 2012-08-12 13:44:07 -0400
  • 458bbdee8f Add useful logger.info telling us the mismatch and indel context sizes Mark DePristo 2012-08-12 10:27:05 -0400
  • 6fefdaf428 "update integration tests in CombineVariantsIntegrationTest" Ami Levy Moonshine 2012-08-10 17:00:35 -0400
  • 4968daf0a5 update integration tests at CombineVariantsIntegrationTest Ami Levy Moonshine 2012-08-10 16:58:05 -0400
  • 1a87f67258 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-10 15:11:12 -0400
  • 40f0320a1c When adding a unit test to LIBS for X and = CIGAR operators, I uncovered a bug with the implementation of the ReadBackedPileup.depthOfCoverage() method. Eric Banks 2012-08-10 14:58:29 -0400
  • eca9613356 Adding support of X and = CIGAR operators to the GATK Eric Banks 2012-08-10 14:54:07 -0400
  • 949ed207ca capMaxAllelesForIndels -> capMaxAltAllelesForIndels Joel Thibault 2012-08-08 15:52:24 -0400
  • b17edaad66 Change memoryValues to List[Double] Joel Thibault 2012-07-31 11:15:54 -0400
  • 32a66b5ae4 Add -nt parameter Joel Thibault 2012-07-31 10:31:17 -0400
  • 2a113977a9 Resolving merge conflicts with the new MD5s Ryan Poplin 2012-08-10 11:47:00 -0400
  • 5f82ffd5d8 Adding LowQual filter to the output of the HaplotypeCaller. Ryan Poplin 2012-08-10 11:25:14 -0400
  • d7d7ccf789 Revert unintentional license change David Roazen 2012-08-09 17:10:47 -0400
  • d56a4631dc Update cofoja version in build.xml David Roazen 2012-08-09 17:08:43 -0400
  • 68fb04b8f7 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable into testing Ami Levy Moonshine 2012-08-09 16:48:22 -0400
  • 3362584014 Updating cofoja to the latest version Mark DePristo 2012-08-09 15:34:20 -0400
  • 06258c8a01 BCF2 optimizations Mark DePristo 2012-08-09 15:34:07 -0400
  • c6bd9b15ff BCF2 optimizations Mark DePristo 2012-08-09 11:09:09 -0400
  • 9a0dda71d4 BCF2 optimizations Mark DePristo 2012-08-09 09:00:44 -0400
  • 9887bc4410 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-09 16:31:06 -0400
  • f4c72a26d5 A few quick, minor findbugs fixes. Ryan Poplin 2012-08-09 16:30:58 -0400
  • c7f22e410f A few quick, minor findbugs fixes. Ryan Poplin 2012-08-09 16:22:08 -0400
  • abb168e1ba Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-08-09 16:09:58 -0400
  • 67d4148b32 Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig. Mauricio Carneiro 2012-08-09 15:58:18 -0400
  • 58420098ac Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-08-09 13:02:23 -0400
  • c6132ebe26 Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test Mauricio Carneiro 2012-08-09 13:02:11 -0400
  • def077c4e5 There's actually a subtle but important difference between foo++ and ++foo Eric Banks 2012-08-09 12:42:50 -0400
  • e48727dae3 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-09 10:31:10 -0400
  • 5be7e0621d Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-09 09:58:34 -0400
  • 71ee8d87b3 Rename per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarify wording in VCF header Guillermo del Angel 2012-08-09 09:58:20 -0400
  • 6230b49a86 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-08 21:44:43 -0400
  • 35cec8530c Make coverage threshold in FindCoveredIntervals a command-line argument Eric Banks 2012-08-08 21:44:24 -0400
  • 250ffd2ad7 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-08-08 15:50:07 -0400
  • 78c1556186 Fixing ReduceReads downsampling bug -- downsampled reads were not being excluded from the read window, causing them to trail back and get caught by the sliding window exception Mauricio Carneiro 2012-08-08 15:49:31 -0400
  • 1223d77546 Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events Ryan Poplin 2012-08-08 15:13:20 -0400
  • 0a2a646a52 Other random FindBugs fixes Eric Banks 2012-08-08 14:56:27 -0400
  • f652d7806e FindBugs found an infinite loop in the code Eric Banks 2012-08-08 14:44:49 -0400
  • 4c84cc9486 Quick pass of FindBugs 'should be static inner class' fixes. Eric Banks 2012-08-08 14:42:06 -0400
  • a0196c9f5b Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes. Eric Banks 2012-08-08 14:34:16 -0400
  • 4b2e3cec0b Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools. Eric Banks 2012-08-08 14:29:41 -0400
  • 3e2752667c Intermediate checkin for ReducedReads with HaplotypeCaller - change min read count over k-mer to average count over k-mer when doing assembly of a reduced read (not optimal, currently trying max and then will decide on best approach), fix merge conflicts Guillermo del Angel 2012-08-08 12:07:33 -0400
  • a7811d673f Update URL for phone home / GATK key documentation output by the GATK upon error David Roazen 2012-08-08 09:29:54 -0400
  • cda8d944b7 Bugfixes for BCF with VQSR Mark DePristo 2012-08-07 17:22:27 -0400
  • 80b94a4f9a AdaptiveContexts implement pruning to a given chi2 p value Mark DePristo 2012-08-07 16:36:57 -0400
  • 982c735c76 VisualizeAdaptiveTree now considers only leaf nodes when computing max/min penalty Mark DePristo 2012-08-07 08:38:16 -0400
  • 15085bf03e The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads. Ryan Poplin 2012-08-07 13:58:22 -0400
  • 2c76f71a03 Update -maxAlleles argument in integration tests Eric Banks 2012-08-06 22:48:04 -0400
  • c66a896b8e Fix UG integration test broken by new -maxAltAlleles nomenclature Guillermo del Angel 2012-08-06 21:29:21 -0400
  • 97c5ed4feb Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-06 20:22:31 -0400
  • 238d55cb61 Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead Guillermo del Angel 2012-08-06 20:22:12 -0400
  • d2feb5d742 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-06 15:06:45 -0400
  • 4b5e1aed1f We might completely overhaul the AssignSomaticStatus tool at some point, but for now I've just tweaked it a little so that it runs well with the TALEN data: fixed VCF header bugs and changed it so that any multi-sample VCF can be used and the user specifies which of the samples is the normal and which should be used as the tumor (only 1 T/N pair allowed now). Eric Banks 2012-08-06 15:06:36 -0400
  • 00858f16a6 Deleting empty unit test for AdaptiveContexts Mark DePristo 2012-08-06 12:57:55 -0400
  • f1c30c3a59 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-06 12:02:26 -0400
  • d85b38e4da Updating HaplotypeCaller integration tests Ryan Poplin 2012-08-06 12:02:19 -0400
  • 44f160f29f indelGOP and indelGCP are now advanced, not hidden arguments Mark DePristo 2012-08-06 11:42:36 -0400
  • 2f004665fb Fixing public -> private dep Mark DePristo 2012-08-06 11:42:12 -0400
  • 7bf5ca51ee Major bugfix for adaptive contexts Mark DePristo 2012-08-04 11:28:17 -0400
  • b4841548f1 Bug fixes and misc. improvements to running the adaptive context tools Mark DePristo 2012-08-03 17:53:46 -0400
  • b8709d8c67 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-06 11:41:28 -0400
  • afa70a13a9 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-06 11:40:27 -0400
  • 973d1d47ed Merging together the computeDiploidHaplotypeLikelihoods functions in the HaplotypeCaller's LikelihoodEngine so they both benefit from the ReducedRead's RepresentativeCount Ryan Poplin 2012-08-06 11:40:07 -0400
  • 210db5ec27 Update -maxAlleles argument to -maxAltAlleles to make it more accurate. The hidden GSA production -capMaxAllelesForIndels argument also gets updated. Eric Banks 2012-08-06 11:31:18 -0400
  • 8f95a03bb6 Prevent NumberFormatExceptions when parsing the VCF POS field Eric Banks 2012-08-06 11:19:54 -0400
  • b7eec2fd0e Bug fixes related to the changes in allele padding. If a haplotype started with an insertion it led to array index out of bounds. Haplotype allele insert function is now very simple because all alleles are treated the same way. HaplotypeUnitTest now uses a variant context instead of creating Allele objects directly. Ryan Poplin 2012-08-05 12:29:10 -0400
  • e1bba91836 Ready for full-scale evaluation adaptive BQSR contexts Mark DePristo 2012-08-03 16:01:27 -0400
  • d2e8eb7b23 Fixed 2 haplotype caller unit tests: a) new interface for addReadLikelihoods() including read counts, b) disable test that test basic DeBruijn graph assembly, not ready yet Guillermo del Angel 2012-08-03 14:26:51 -0400
  • c3b6e2b143 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-03 13:14:43 -0400
  • ff80f17721 Using PathComparatorTotalScore in the assembly graph traversal does a better job of capturing low frequency branches that are inside high frequnecy haplotypes. Ryan Poplin 2012-08-03 13:14:37 -0400
  • 6f8e7692d4 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-03 12:24:37 -0400
  • 9e25b209e0 First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller Guillermo del Angel 2012-08-03 12:24:23 -0400
  • 8817fc70d1 Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-03 10:45:01 -0400
  • f40d0a0a28 Updating VQSR to work with the MNP and symbolic variants that are coming out of the HaplotypeCaller. Integration tests change because of the MNPs in dbSNP. Ryan Poplin 2012-08-03 10:44:36 -0400
  • 51bd03cc36 Add RemoveProgramRecords annotation to ActiveRegionWalker Joel Thibault 2012-08-02 14:46:00 -0400
  • addbfd6437 Add a RemoveProgramRecords annotation Joel Thibault 2012-08-02 14:21:30 -0400
  • 524d7ea306 Choose whether to keep program records based on Walker Joel Thibault 2012-07-31 15:09:36 -0400
  • e04989f76d Bugfix for new PASS position in dictionary in BCF2 Mark DePristo 2012-08-03 09:42:21 -0400
  • d22b8cf86b VisualizeContextTree now loops over M, I, and D states generating trees and analyzes Mark DePristo 2012-08-02 16:45:13 -0400
  • fb5dabce18 Update BCF2 to include a minor version number so we can rev (and report errors) with BCF2 Mark DePristo 2012-08-02 16:44:39 -0400
  • b4f4d86c77 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-02 11:49:03 -0400
  • 3ece4c4993 Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-02 11:41:36 -0400
  • 6f7a236cfc Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Ryan Poplin 2012-08-02 11:41:20 -0400
  • cb8bc18aeb Fix for error in HaplotypeCaller. HC has a UG argument collection for the UG engine but some of those arguments aren't appropriate to set. Ryan Poplin 2012-08-02 11:41:06 -0400
  • e3f89fb054 Missing/malformed GATK report files are user errors Eric Banks 2012-08-02 11:33:21 -0400
  • cc01f844d4 Merged bug fix from Stable into Unstable Eric Banks 2012-08-02 11:25:28 -0400