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  • 1473e166f7 Update VariantCallQC script Mark DePristo 2012-04-04 14:50:25 -0400
  • 2cc1e8d871 PostCallingQC uses IndelLengthHistogram now Mark DePristo 2012-04-04 14:29:09 -0400
  • fcdd65a0f4 Bugfix for IndelLengthHistogram Mark DePristo 2012-04-04 14:28:49 -0400
  • 3593996a87 G1K summary table needs to use the -keepAC0 flag Mark DePristo 2012-04-04 14:07:03 -0400
  • 1ccea866d8 VariantEval now includes -keepAC0 argument to include sites with alt alleles but AC 0 in analyses Mark DePristo 2012-04-04 13:17:19 -0400
  • 15e26fec04 Many cosmetic fixes to pool caller (not done yet): better docs, some code reorganization, change iterator inside PoolGenotypeLikelihoods so that we store conformations and convert to/from PL vectors in the same order as the non-pool case (it used to be flipped), to maintain better legibility. Improved unit tests (not done yet) Guillermo del Angel 2012-04-04 15:08:19 -0400
  • 9e32a975f8 Wow, symbolic alleles were all busted internally and this finally bubbled up after my previous commit. For some reason we were inconsistently forcing allele trimming/padding if one was present. Not anymore. Eric Banks 2012-04-04 13:47:59 -0400
  • 337ff7887a When constructing VariantContexts from symbolic alleles, check for the END tag in the INFO field; if present, set the stop position of the VC accordingly. Added integration test to ensure that this is working properly for use with -L intervals. Eric Banks 2012-04-04 10:57:05 -0400
  • 1248f9025d Clean up and fix bug in PoolGenotypeLikelihoodsUnitTest. b) Cosmetic fixes to PoolAFCalculationModel, don't print PL vectors per pool if they're too long or else vcf's are too hard to make sense of Guillermo del Angel 2012-04-03 21:27:53 -0400
  • 05d8400468 Fix up broken non-pool UG tests: GenotypeLikelihoods.calcNumLikelihoods now expects total # of alleles, not # of alt ones. Add doc to new function implementation. Add unit test for function. Add unit test for PoolGenotypeLikelihoods (not fully done yet) Guillermo del Angel 2012-04-03 20:51:24 -0400
  • 5a10f173ea Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow) Guillermo del Angel 2012-04-03 18:55:52 -0400
  • 61e1ec6cdd More bug fixing PoolAFCalculationModel Guillermo del Angel 2012-04-03 18:12:39 -0400
  • baad840598 Bug fixing PoolAFCalculationModel Guillermo del Angel 2012-04-03 17:03:42 -0400
  • 5abb07da5d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-04-03 17:00:45 -0400
  • 4d33f63986 Bug fixing PoolAFCalculationModel Guillermo del Angel 2012-04-03 16:58:12 -0400
  • a6837d31d4 Success! A fast and low-memory converter from VCF into a binary ped file. This is mostly so I don't have to listen to Pierre/Jason complain about how slow and inefficient plinkseq is at converting; or at transposting. This automatically writes to individual-major mode. It will eat up space on /tmp if you don't run with -Djava.io.tmpdir, so be careful if you use it. Christopher Hartl 2012-04-03 16:13:16 -0400
  • 63b1e737c6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-04-03 15:43:50 -0400
  • 9e11b4f9a7 Major refactor/completion of new Pool Caller under UnifiedGenotyper framework. PoolAFCalculationModel implements new math to combine pools - correct, but still O(N^2) and not complete yet for multiallelics. Pool likelihoods are better encapsulated and kept in an internal hashmap from int[] -> double for space efficiency (likelihoods can be big for pool calls when in initial discovery mode with 4 alleles). Maybe need several iterations of optimization to make it runnable at large scale. Still need to correct function chooseMostLikelyAlternateAlleles before full runs can be produced. Guillermo del Angel 2012-04-03 15:43:32 -0400
  • f9ce9962c4 Minor changes to verbose mode Eric Banks 2012-04-03 10:53:48 -0400
  • 8ca4df38ed Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-04-02 22:47:19 -0400
  • f6aa95685d OutOfMemory exceptions are User Errors Eric Banks 2012-04-02 22:46:56 -0400
  • 659b82e74d Old -B syntax is long gone at this point. Safe to remove the warning. Eric Banks 2012-04-02 22:25:16 -0400
  • 0b37c556f5 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-04-02 15:05:08 -0400
  • 02a9b73360 Bug fix for Solid reads still triggering the active region traversal at nearly every locus. Ryan Poplin 2012-04-02 15:04:17 -0400
  • 326220c91c Removing extended event related unit tests Eric Banks 2012-04-02 14:40:36 -0400
  • 99d27ddcc4 Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. Eric Banks 2012-04-02 14:27:36 -0400
  • 4075bc7d3d BUGFIX to not skip chr22 Mark DePristo 2012-04-02 09:14:07 -0400
  • 6b7a00061a VariantsToTable now works with multiple input VCFs Mark DePristo 2012-04-02 09:13:35 -0400
  • 8072060496 Update g1K summary table to actually work with autosome / X distinction Mark DePristo 2012-04-01 16:10:39 -0400
  • f05cc96991 Adding multiallelics and phased variant examples to the HaplotypeCaller integration tests. Lowering max alternate alleles back to the UG default value because of memory constraints with many samples. Ryan Poplin 2012-03-31 10:53:37 -0400
  • 4f73ea902f Final update for VE. VCFStreaming wasn't yet updated Mark DePristo 2012-03-30 21:52:01 -0400
  • c9b2e376d3 Change variable name from Count to Freq in variantCallQC.R Mark DePristo 2012-03-30 20:11:59 -0400
  • fbbb8509ad Final commits to VariantEval Mark DePristo 2012-03-30 20:11:06 -0400
  • f997b1dbf9 Don't allow active region paths with cycles because it leads to Smith-Waterman issues Ryan Poplin 2012-03-30 16:06:40 -0400
  • 4b45a2c99d Final version of new VariantEval infrastructure. Mark DePristo 2012-03-30 15:28:47 -0400
  • 8c0718a7c9 Fixed missing import Mark DePristo 2012-03-30 08:58:08 -0400
  • 976bac0452 BaseTest now has a global variable to turn off network connection requirement Mark DePristo 2012-03-30 08:34:35 -0400
  • 097ed4ecc4 Memory usage optimizations and safety improvements to StratNode and StratificationManager Mark DePristo 2012-03-30 08:32:48 -0400
  • b335c22f6d Fully refactored, mostly cleaned up version of VariantEval using StratificationManager Mark DePristo 2012-03-29 10:34:41 -0400
  • c8086a79e3 New StratificationManager based VariantEval passes unmodified integration tests Mark DePristo 2012-03-29 09:46:55 -0400
  • d37f31e349 First version of VariantEval that runs (approximately correctly) with new StratificationManager Mark DePristo 2012-03-29 07:06:09 -0400
  • 8971b54b21 Phase II of Stratification manager Mark DePristo 2012-03-28 14:18:56 -0400
  • 9f1cd0ff66 Lots of new functionality for StratificationStates manager Mark DePristo 2012-03-28 12:55:29 -0400
  • 91c5353c4c By default use 4 threads for 1000G table Mark DePristo 2012-03-27 17:51:37 -0400
  • a3d896d80e Part I of creating a fast state space lookup for VE Mark DePristo 2012-03-27 17:13:24 -0400
  • a36f4570c4 Adding two new output options in HaplotypeCaller for Menachem. The first controls the look ahead distance for turning consecutive SNPs into MNPs and the second outputs the full haplotype sequence for the active region instead of using Smith Waterman to find all the variants and output them in individual VCF records. Ryan Poplin 2012-03-30 14:09:38 -0400
  • 11645568a8 Removed all functional code from PoolIndelGenotypeLikelihoodsCalculationModel - it was just copied over from non-pool version. Real pool indel functionality not ready yet. Several pool caller cleanups and tmp additions Guillermo del Angel 2012-03-30 10:42:32 -0400
  • 533c283783 Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine. Eric Banks 2012-03-30 10:37:14 -0400
  • 6b49af253b Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there. Eric Banks 2012-03-30 10:33:30 -0400
  • b467cd1dae Removing dependence on extended events for the remaining Variant Annotator modules. Eric Banks 2012-03-30 09:05:26 -0400
  • b21889812d Removing some more usages of extended events. Not done yet, but almost there. Eric Banks 2012-03-30 01:51:37 -0400
  • ad6ace2439 Resolving merge conflicts Eric Banks 2012-03-30 01:51:09 -0400
  • 16bef191c6 UG integration tests updated. A handful of sites are lost because there are only 5 indels and one starts at the beginning of the read so it no longer passes our min threshold (now consistent with GGA), but mostly the depth changes ever so slightly once in a while between extended and normal pileups (I think the normal pileups are correct). I have looked thoroughly in IGV at ALL differences and am happy with the new results. As an aside, the AD is now calculated more accurately for indels. Eric Banks 2012-03-30 01:35:49 -0400
  • f4d4969f23 Don't ever return null for the list of GL models Eric Banks 2012-03-30 00:22:40 -0400
  • 44ac49aa34 Removing dependencies in the annotations on extended events. Some refactoring involved in this. Eric Banks 2012-03-30 00:17:02 -0400
  • 962fc352ae unnecessary substitution. Mauricio Carneiro 2012-03-29 18:01:43 -0400
  • b7c59d5d43 this was a dummy test I was using to figure out what the problem was. Deleting it. Mauricio Carneiro 2012-03-29 18:00:25 -0400
  • cbd21c6339 Nasty, nasty..... Mauricio Carneiro 2012-03-29 17:49:42 -0400
  • c2e27729c7 Renaming PileupElement.isBeforeDeletion() to PileupElement.isBeforeDeletedBase() so that it's more clear that it can still be true while inside a deletion. Added PileupElement.isBeforeDeletionStart() to cover the case that I want where we only trigger before the actual deletion event. Similarly for after a deletion. Updated counting code in ConsensusAlleleCounter accordingly. Eric Banks 2012-03-29 17:08:25 -0400
  • 6da9571829 resolving merge conflicts. Ryan Poplin 2012-03-29 16:16:28 -0400
  • ca96544ed0 All the zero quality N bases in the solid reads are adding lots of extra paths in the assembly graph. We now require a minimum base quality for every base in the kmer before adding it to the graph. The large number of solid reads with unmapped mates was also triggering the active region traversal at every base. We now ignore that check for solid reads. Ryan Poplin 2012-03-29 16:14:29 -0400
  • e4469a83ee First attempt at removing all traces of extended events from UG; integration tests are expected to fail. Eric Banks 2012-03-29 14:59:29 -0400
  • e61e162c81 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-03-29 12:33:13 -0400
  • cf364f26a0 Fixing alignment issue with the GATKReportColumn algorithm Mauricio Carneiro 2012-03-29 12:27:23 -0400
  • f80bd4276a fixed estimated Q reported calculation in the gatherer Mauricio Carneiro 2012-03-29 09:53:47 -0400
  • 8a9fb514b6 simplifying GATKReportColumn constructor logic Mauricio Carneiro 2012-03-29 09:34:38 -0400
  • e861106398 Accidentally erased important line Eric Banks 2012-03-29 11:08:54 -0400
  • e4a225ed09 Move the code to subset a Variant Context to fewer alleles (including restructuring the PLs appropriately) into VariantContextUtils where it can be used generally. Eric Banks 2012-03-29 11:07:37 -0400
  • c9c3f6b0fc Minor UG Engine refactoring/cleanup: instead of passing in the # of samples separately from sample set, pass in ploidy instead and compute # of chromosomes internally - will help later on with code clarity Guillermo del Angel 2012-03-29 11:05:42 -0400
  • 9684a2efb0 HaplotypeCaller: Variants found on the same haplotype are now written out with phased genotypes. There are serious eval issues with MNPs so disabling them for now. Ryan Poplin 2012-03-29 09:41:29 -0400
  • a0843f125e Forgot to add file itself for new unit test Guillermo del Angel 2012-03-28 21:08:18 -0400
  • 250adca350 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-28 21:01:49 -0400
  • e0ab4e4b30 Refactoring so that ConsensusAlleleCounter can use regular pileups and can operate correctly. This involved adding utility functions to ReadBackedPileup to count # of insertions/deletions right after current position. Added unit test for IndelGenotypeLikelihoods, esp. ConsensusAlleleCounter logic Guillermo del Angel 2012-03-28 21:01:31 -0400
  • 8f0e9d74ce GATKReportTable output refactor Mauricio Carneiro 2012-03-28 16:56:40 -0400
  • 5ff24f8cf3 We want the DoC calculations for CNVs to include N bases in the reference just so that the PAR regions in chr Y (set to all Ns) end up with mean coverage of 0/L, where L = target length (and not NaN = 0/0). Including Ns in any other targets is probably OK too, since most (if not all) non-chromosome Y targets will not have any Ns Menachem Fromer 2012-03-28 16:42:34 -0400
  • 62ee31afba Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-28 16:00:38 -0400
  • 1eee9d512d Make computeConsensusAlleles protected inside IndelGenotypeLikelihoodsCalculationModel so we can use it in unit tests, b) make ConsensusAlleleCounter work if no extended event pileup is present (necessary for ext. event removal) Guillermo del Angel 2012-03-28 15:41:39 -0400
  • 4a396d357d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-28 15:37:33 -0400
  • c17e2c61ef Adding more assembly unit tests Ryan Poplin 2012-03-28 15:37:18 -0400
  • bb36cd4adf Quick fixes to BQSRGatherer and GATKReportTable Mauricio Carneiro 2012-03-27 22:51:21 -0400
  • 63cf7ec7ec Added more primitives to GATK Report Column Type Roger Zurawicki 2012-03-27 16:22:21 -0400
  • d2586911a4 Forgot to add tolerance to new MathUtils unit tests Guillermo del Angel 2012-03-28 08:18:36 -0400
  • 08f7d47d7c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-28 07:42:09 -0400
  • 7f211c66fa Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-27 23:09:18 -0400
  • 60c9ada5d8 Adding some basic AssemblyEngine unit tests. Ryan Poplin 2012-03-27 23:09:04 -0400
  • 12aa72f200 Merged bug fix from Stable into Unstable Mark DePristo 2012-03-27 22:43:00 -0400
  • 979a84a252 Bugfix for thread unsafe PL cache Mark DePristo 2012-03-27 22:42:30 -0400
  • 8f34412fb8 First Pool Caller exact model: silly straightforward math implementation of biallelic pool caller exact likelihood model, no attempt and any smartness or optimization, no support yet for generalized multiallelic form, just hooking up for testing Guillermo del Angel 2012-03-27 20:59:44 -0400
  • 74615c42df Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-27 15:19:46 -0400
  • 80b11cfe3c Bug fix for the case of zero reads remaining in the active region after clipping and filtering. Ryan Poplin 2012-03-27 15:19:34 -0400
  • ed322bd73f Fix again merge issues Guillermo del Angel 2012-03-27 15:03:13 -0400
  • b4a7c0d98d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-27 15:01:03 -0400
  • 343a061b1c Fix merge issues when incorporating new AF calculations changes Guillermo del Angel 2012-03-27 15:00:44 -0400
  • 1b75663178 BQSR Gatherer implementation and integration tests Mauricio Carneiro 2012-03-23 17:17:32 -0400
  • ea9c04b8c2 Updated license year Joel Thibault 2012-03-27 14:32:02 -0400
  • 5dbd3625cd Initial algorithm for choosing best alternate haplotypes to genotype based on the likelihoods from all samples instead of choosing for each sample independently. Simple tradeoff of penalty for increasing model complexity and likelihood of the data. Ryan Poplin 2012-03-27 13:38:52 -0400
  • c112e0824a I was adding verbose output to the Pileup output for a one-off and decided that I might as well commit it as an option. Updated deprecated calls while I was in there. Eric Banks 2012-03-27 11:09:03 -0500
  • a638996fe2 Cleanup of VariantEval, diatribe about performance problems with StateKey Mark DePristo 2012-03-27 11:56:24 -0400
  • 679bb03014 Simple utility function for converting an Iterable<T> to Collection<T> Mark DePristo 2012-03-27 11:54:58 -0400
  • 1f5f737c8b Optimizing the GATKReportTable.write Mark DePristo 2012-03-27 11:54:35 -0400