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  • 92c5635e19 Cleanup, document, and unit test ActiveRegion Mark DePristo 2013-01-28 11:53:43 -0500
  • 3d9a83c759 BaseCoverageDistributions should be 'by reference' Mauricio Carneiro 2013-01-29 22:36:31 -0500
  • e02dac03aa Fix use of fully-qualified package name in the HybridSelectionPipeline David Roazen 2013-01-29 20:52:24 -0500
  • 6449c320b4 Fix the CachingIndexedFastaSequenceFileUnitTest David Roazen 2013-01-29 20:30:36 -0500
  • 29fd536c28 Updating licenses manually Mauricio Carneiro 2013-01-29 17:27:53 -0500
  • 0be5c66b61 Fixing return value of the license check script Mauricio Carneiro 2013-01-29 17:17:42 -0500
  • a536e1da84 Move some VCF/VariantContext methods back to the GATK based on feedback David Roazen 2013-01-29 13:57:39 -0500
  • 581df64197 Updating Licensing scripts not to panic when removing files Mauricio Carneiro 2013-01-29 16:47:09 -0500
  • a1908a0eca Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-29 16:33:20 -0500
  • 4aaef495c6 correct the help message Ami Levy-Moonshine 2013-01-29 16:33:12 -0500
  • e4ec899a87 First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs! Eric Banks 2013-01-29 15:51:07 -0500
  • cba89e98ad Refactoring the Bayesian empirical quality estimates to be in a single unit-testable function. Ryan Poplin 2013-01-29 15:50:46 -0500
  • 1d5b29e764 Unit tests for repeat covariates: generate 100 random reads consisting of tandem repeat units of random content and size, and check that covariates match expected values at all positions in reads. Fixed corner case where value of covariate at border between 2 tandem repeats of different length/content wasn't consistent Guillermo del Angel 2013-01-29 15:23:02 -0500
  • c11197e361 Refactored repeat covariates to eliminate duplicated code - now all inherit from basic RepeatCovariate abstract class. Comprehensive unit tests coming... Guillermo del Angel 2013-01-29 10:10:24 -0500
  • 35543b9cba updating BQSR integration test values for the PR half of BQSR. Ryan Poplin 2013-01-29 09:47:57 -0500
  • bf25196a0b Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-28 22:33:13 -0500
  • e9c3a0acdf fix typo Ryan Poplin 2013-01-28 22:18:58 -0500
  • 1f254d29df Don't set the empirical quality when reading in the recal table because then we won't be using the new quality estimates for the prior since the value is cached. Ryan Poplin 2013-01-28 22:16:43 -0500
  • a8a68697f1 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-28 20:18:51 -0500
  • ff799cc79a Fixed bad merge Guillermo del Angel 2013-01-28 20:04:25 -0500
  • 5995f01a01 Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet: a) Add option to stratify CalibrateGenotypeLikelihoods by repeat - will add integration test in next push. b) Simulator to produce BAM files with given error profile - for now only given SNP/indel error rate can be given. A bad context can be specified and if such context is present then error rate is increased to given value. c) Rewrote RepeatLength covariate to do the right thing - not fully working yet, work in progress. d) Additional experimental covariates to log repeat unit and combined repeat unit+length. Needs code refactoring/testing Guillermo del Angel 2013-01-28 19:55:46 -0500
  • 3f5c2e4989 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-28 19:04:52 -0500
  • c103623cf6 bug fix in my new function at SampleUtils.java Ami Levy-Moonshine 2013-01-28 19:04:39 -0500
  • c2e580b252 Fixing SplitReads chopping unit tests Mauricio Carneiro 2013-01-28 16:21:17 -0500
  • d665a8ba0c The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior. Ryan Poplin 2013-01-28 15:56:33 -0500
  • 8777e02aa5 R issue in Queue fixed. Tad Jordan 2013-01-28 11:33:49 -0500
  • aab160372a No need to sort the BQSR tables by default. Ryan Poplin 2013-01-28 11:26:01 -0500
  • f63f27aa13 org.broadinstitute.variant refactor, part 2 David Roazen 2013-01-08 14:45:50 -0500
  • 1599c9a20e Remove the ability to package GATK/Queue Lite from the build system David Roazen 2013-01-28 02:40:18 -0500
  • 3744d1a596 Collapse the downsampling fork in the GATK engine David Roazen 2013-01-28 01:19:44 -0500
  • 5003deafb6 Fixing split-reads unit tests Mauricio Carneiro 2013-01-27 23:37:56 -0500
  • 1aee8f205e Tool to calculate per base coverage distribution Mauricio Carneiro 2013-01-27 16:48:44 -0500
  • 63913d516f Add join call to Progress meter unit test so we actually know the daemon thread has finished Mark DePristo 2013-01-27 16:52:45 -0500
  • f5473285d5 Update CountReadsInActiveRegions md5 Mark DePristo 2013-01-27 14:35:55 -0500
  • 14d8afe413 Remove startSearchAt state variable from ActivityProfile Mark DePristo 2013-01-27 13:51:53 -0500
  • c97a361b5d Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF Mark DePristo 2013-01-27 13:39:35 -0500
  • 72b2e77eed Linearize the findEndOfRegion algorithm in ActivityProfile, radically improving its performance Mark DePristo 2013-01-26 15:23:40 -0500
  • 0fb238b61e TraverseActiveRegions Optimizations and Bugfixes: make sure to record position of current locus to discharge active regions when there's no data Mark DePristo 2013-01-25 17:25:42 -0500
  • 804caf7a45 HaplotypeCaller Optimization: return a inactive (p = 0.0) activity if the context has no bases in the pileup Mark DePristo 2013-01-25 17:23:15 -0500
  • 93d88cdc68 Optimization: LocusReferenceView now passes along the contig index to createGenomeLoc, speeding up their creation Mark DePristo 2013-01-25 17:21:05 -0500
  • 52a28968a9 ART optimization: BandPassActivityProfile only applies the gaussian filter if the state probability > 0 Mark DePristo 2013-01-25 17:20:13 -0500
  • 705cccaf63 Making SplitReads output FastQ's instead of BAM Mauricio Carneiro 2013-01-27 02:36:31 -0500
  • ae38cf3f72 Adding read directionality to SplitReads Mauricio Carneiro 2013-01-26 22:25:56 -0500
  • 6ea7133d95 Updating licenses of latest moved files Mauricio Carneiro 2013-01-26 13:21:25 -0500
  • ef4cc742e5 Fixing the licensing scripts Mauricio Carneiro 2013-01-26 12:36:30 -0500
  • e7c9e3639e Making metrics a required parameter in MarkDuplicates Mauricio Carneiro 2013-01-25 17:49:15 -0500
  • 99cb8d68e9 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-25 16:07:38 -0500
  • b8c0b05785 Add contract to ensure that getAdapterBoundary returns the right result Mark DePristo 2013-01-25 16:00:06 -0500
  • e445c71161 LIBS optimization for adapter clipping Mark DePristo 2013-01-24 16:36:55 -0500
  • f50db01742 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-25 15:55:56 -0500
  • b4447cdca2 In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample). Now we will check it only in CombineVariants.init using the headers. A new function was added to SamplesUtils with unitTests in CVunitTest.java. Ami Levy-Moonshine 2013-01-25 15:49:51 -0500
  • c58e02a3bd Added a QFunction.jobLocalDir for optionally tracking a node local directory that may have faster intermediate storage, with SGF ensuring that if the directory happens to be on the same machine that it get's a clone specific sub-directory to avoid collisions. Khalid Shakir 2013-01-25 14:16:39 -0500
  • fc22a5c71c Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-25 11:47:38 -0500
  • eaf6279d48 adding RBP to the general calling pipeline and few other small changes to it (to make it run with the current bundel file names Ami Levy-Moonshine 2013-01-25 11:47:30 -0500
  • 3f95f39be3 Updating HC md5s for new cutting algorithm and default band pass filter parameters Mark DePristo 2013-01-25 11:06:47 -0500
  • 008b617577 Cleanup the getLIBS function in LocusIterator Mark DePristo 2013-01-25 10:13:12 -0500
  • f7b80116d6 Don't let users play with the different exact model implementations. Eric Banks 2013-01-25 10:52:02 -0500
  • 6dd0e1ddd6 Pulled out the --regenotype functionality from SelectVariants into its own tool: RegenotypeVariants. This allows us to move SelectVariants into the public suite of tools now. Eric Banks 2013-01-25 09:42:04 -0500
  • c7a29b1d39 Fixed NPE in ActiveRegionUnitTest by allowing null supporting states in ActiveRegion Mark DePristo 2013-01-24 13:47:16 -0500
  • 592f90aaef ActivityProfile now cuts intelligently at the best local minimum when in a larger than max size active region Mark DePristo 2013-01-24 11:28:02 -0500
  • c96b64973a Soft clip probability propagation is capped by the MAX_PROB_PROPAGATION_DISTANCE, which is 50 bp Mark DePristo 2013-01-23 15:52:00 -0500
  • 0c94e3d96e Adaptively compute the band pass filter from the sigma, up to a maximum size of 50 bp Mark DePristo 2013-01-23 15:41:56 -0500
  • 9e43a2028d Making band pass filter size, sigma, active region max size and extension all accessible from the command line Mark DePristo 2013-01-23 14:50:14 -0500
  • cd91e365f4 Optimize getCurrentContigLength and getLocForOffset in ActivityProfile Mark DePristo 2013-01-23 14:13:21 -0500
  • 26ef400f85 More reviews Eric Banks 2013-01-24 13:20:12 -0500
  • 6790e103e0 Moving lots of walkers back from protected to public (along with several of the VA annotations). Let's see whether Mauricio's automatic git hook really works! Eric Banks 2013-01-24 11:42:49 -0500
  • 9e003b3296 more updates to the licensing scripts Mauricio Carneiro 2013-01-23 23:54:23 -0700
  • e1c1a4de4c Moving licensing scripts to bash instead of tcsh Mauricio Carneiro 2013-01-23 21:50:38 -0700
  • 42b056e8ea Forgot the unit test. Mauricio Carneiro 2013-01-23 21:18:27 -0700
  • 36c7c418e6 Adding the licenses to the files Mauricio Carneiro 2013-01-23 21:15:06 -0700
  • 243fcde840 Adding license to SplitReads Mauricio Carneiro 2013-01-23 21:12:36 -0700
  • 643a508564 Added atlassian intellij plugin file to .gitignore Mauricio Carneiro 2013-01-23 20:53:36 -0700
  • a4fbf9df1e SplitReads walker implementation (for AGBT talk) Mauricio Carneiro 2013-01-23 20:16:23 -0700
  • a3b98daf1a Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Chris Hartl 2013-01-23 14:49:34 -0500
  • 7fcfa4668c Since GenotypeConcordance is now a standalone walker, remove the old GenotypeConcordance evaluation module and the associated integration tests. Chris Hartl 2013-01-23 14:47:23 -0500
  • fc54a5da55 Adding the new bash script Mauricio Carneiro 2013-01-23 12:14:34 -0700
  • 6588b4bacd tcsh -> bash Mauricio Carneiro 2013-01-23 12:08:49 -0700
  • 8e8993da27 oops... forgot to change sys.argv to filename Mauricio Carneiro 2013-01-23 12:01:06 -0700
  • 820bec5572 Dropping xargs Mauricio Carneiro 2013-01-23 11:53:43 -0700
  • ee8039bf25 Fix trivial call in unit test Mark DePristo 2013-01-23 13:51:58 -0500
  • 09edc6baeb TraverseActiveRegions now writes out very nice active region and activity profile IGV formatted files Mark DePristo 2013-01-23 13:44:40 -0500
  • 8026199e4c Updating md5s for CountReadsInActiveRegions and HaplotypeCaller to reflect new activity profile mechanics Mark DePristo 2013-01-23 09:47:22 -0500
  • 8e8126506b Renaming IncrementalActivityProfile to ActivityProfile Mark DePristo 2013-01-23 09:44:46 -0500
  • e917f56df8 Remove old ActivityProfile and old BandPassActivityProfile Mark DePristo 2013-01-22 16:02:09 -0500
  • 7fd27a5167 Add band pass filtering activity profile Mark DePristo 2013-01-22 15:40:09 -0500
  • eb60235dcd Working version of incremental active region traversals Mark DePristo 2013-01-18 16:57:28 -0500
  • ce160931d5 Optimize creation of reads in ArtificialBAMBuilder Mark DePristo 2013-01-18 16:52:49 -0500
  • e050f649fd IncrementalActivityProfile, complete with extensive unit tests Mark DePristo 2013-01-18 10:18:04 -0500
  • 8d9b0f1bd5 Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile Mark DePristo 2013-01-17 17:31:56 -0500
  • 42b807a5fe Unit tests for ActivityProfileResult Mark DePristo 2013-01-17 14:51:26 -0500
  • 5c16f57690 Reduce the size of the shell blob Mauricio Carneiro 2013-01-23 11:41:18 -0700
  • 002c0085a7 More reviews of false positive sites incorrectly annotated as polymorphic (mostly by HM3). (for some reason I can't get reviews to work in IGV) Eric Banks 2013-01-23 13:21:30 -0500
  • c5e1bb678b Refrain from pushing symlinks into the repo... not all filesystems treat it correctly Mauricio Carneiro 2013-01-22 15:18:19 -0700
  • c500e1d8ac Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Chris Hartl 2013-01-22 15:31:30 -0500
  • d33c755aea Adding docs. Chris Hartl 2013-01-22 15:29:33 -0500
  • 7060e01a8e Fix for broken unit test plus some minor changes to comments. Unit tests were broken by my pulling the site status utility function into the enum. Thankfully the unit tests caught my silly duplication of a line. Chris Hartl 2013-01-22 15:14:41 -0500
  • 3f6cb609c9 Bug fix for AssessNA12878: don't NPE out when using -typesToInclude Eric Banks 2013-01-22 10:42:52 -0500
  • e939e0d9b3 Small improvement to the license update scripts Mauricio Carneiro 2013-01-21 16:19:31 -0500
  • 35e3939dca Adding bamboo script to check all licenses Mauricio Carneiro 2013-01-21 15:59:09 -0500
  • 35f8dc7426 Accept spaces before comments or package line Mauricio Carneiro 2013-01-18 16:51:01 -0500