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  • cadff40247 getRefCoordSoftUnclippedStart and End refactor Mauricio Carneiro 2011-12-20 14:58:18 -0500
  • 07128a2ad2 ReadUtils cleanup Mauricio Carneiro 2011-12-20 14:35:33 -0500
  • 1c4774c475 Static versions of the hard clipping utilities Mauricio Carneiro 2011-12-20 14:30:06 -0500
  • f73ad1c2e2 Bugfix/Rewrite: Algorithm to determine adaptor boundaries Mauricio Carneiro 2011-12-19 14:13:55 -0500
  • 2e88c7fe61 Refactored forest.R to enable loading and testing of goNL and Autism data. RF looks really good on these data sets! Mark DePristo 2011-12-20 16:41:07 -0500
  • b472bab54e Minor changes in default thread values Mark DePristo 2011-12-20 08:59:32 -0500
  • 992d2fa632 Don't print unnecessary debugging info in GATKPerformanceOverTime.R Mark DePristo 2011-12-20 11:08:55 -0500
  • a7891b7a2e Enabling VariantEval reports Mark DePristo 2011-12-19 15:50:43 -0500
  • 0cc5c3d799 General improvements to Queue Mark DePristo 2011-12-19 15:46:32 -0500
  • 7204fcc2c3 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-20 12:59:11 -0500
  • 8ade2d6ac2 max_alternate_alleles also ready to be made public Eric Banks 2011-12-20 12:59:02 -0500
  • 6f52bd580b --multiallelic mode is not hidden anymore (but it is annotated as advanced); added docs Eric Banks 2011-12-20 12:47:38 -0500
  • 37e0044c48 Removing unclipSoftClipBases from ReadUtils Mauricio Carneiro 2011-12-20 00:11:26 -0500
  • 78d9bf7196 Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper Mauricio Carneiro 2011-12-19 14:56:19 -0500
  • 24585062f8 Merge branch 'incoming' Christopher Hartl 2011-12-19 23:16:36 -0500
  • 67298f8a11 AFCR made public (for use in VSS) Minor changes to ValidationSiteSelector logic (SampleSelectors determine whether a site is valid for output, no actual subset context need be operated on beyond that determination). Implementation of GL-based site selection. Minor changes to EJG. Christopher Hartl 2011-12-19 23:14:26 -0500
  • 2d619d8633 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-19 15:38:02 -0500
  • 06d385e619 Simplifying the interface a bit Eric Banks 2011-12-19 15:29:46 -0500
  • 52b8d74e49 Ooops, turning it off until I choose better BAM files to test Mauricio Carneiro 2011-12-19 14:41:46 -0500
  • 339ef92eac Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested. Christopher Hartl 2011-12-19 12:18:18 -0500
  • 8d55c5ea14 Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2011-12-19 12:17:55 -0500
  • fb9950f3ad Integration tests for ReduceReads Mauricio Carneiro 2011-12-19 11:53:54 -0500
  • 758b672c43 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-12-19 17:06:26 +0100
  • 418d22b67e Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2011-12-19 10:59:18 -0500
  • 69661da37d Moving ValidationSiteSelector to validation package in public under my ownership. JunctionGenotyper added and modified several times, this commit is due to merging conflix fixes. Christopher Hartl 2011-12-19 10:57:28 -0500
  • 85dc2239ad Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-12-19 16:53:07 +0100
  • cd28390f52 Merge branch 'yamagishi' Mark DePristo 2011-12-19 10:52:57 -0500
  • 31ac6b063b Complete restructuring of performance script to use local (SSD) cached data on gsa4 Mark DePristo 2011-12-19 10:51:26 -0500
  • d5d0e94a11 a) Updating for posterity original scripts for VQSR project consensus (snp and indel) so that they use newest GATK syntax (also they were not run in the end). b) New scripts for redoing indel GL's, jobs are split per sample and per chromosome. Another script (PhaseIndelRedoCombining.scala) does the combining of all pieces - not the best solution, but best for development/debugging to have two separate entities. c) Experimental walker to assess GL concordance of two callsets - just accumulates squared error between each sample and site GL's and outputs at the end. d) Another one-off to fill a callset of given GL's with greedy genotypes (genotype that maximizes PL) to have more meaningful metrics and QC of a given GL file. Guillermo del Angel 2011-12-19 16:50:52 +0100
  • b0c2f223ab Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-19 10:45:27 -0500
  • 16cc2b864e - Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT Laurent Francioli 2011-12-19 13:41:47 +0100
  • 5fd19ae734 Commented exactly how the results are represented from the exact model so developers can know how to use them. Eric Banks 2011-12-19 10:19:00 -0500
  • 5383c50654 Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R Mark DePristo 2011-12-19 10:08:38 -0500
  • 3069a689fe Bug fix: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case. Eric Banks 2011-12-19 10:04:33 -0500
  • 728d66cca4 Adding Picard imports to the Haplotype Caller Mauricio Carneiro 2011-12-19 09:47:48 -0500
  • 5b678e3b94 Remove ClippingOp UnitTests Mauricio Carneiro 2011-12-18 12:26:06 -0500
  • 1ead00cac5 New fork of SamFileHeaderMerger should be cached at the thread level to enable fast (and valid) thread lookups. Matt Hanna 2011-12-18 19:04:26 -0500
  • bc842ab3a5 Adding option to VariantAnnotator to do strict allele matching when annotating with comp track concordance. Ryan Poplin 2011-12-18 15:27:23 -0500
  • 953998dcd0 Now that getSampleDB is public in the walker base class this override in VariantAnnotator isn't necessary. Ryan Poplin 2011-12-18 14:38:59 -0500
  • 76bd13a1ed Forgot to update the unit test Eric Banks 2011-12-18 01:13:49 -0500
  • 07f9d14d9f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-18 00:43:15 -0500
  • 4d11b20118 updating HC test too Eric Banks 2011-12-18 00:43:01 -0500
  • c5ffe0ab04 No reason to sum the normalized posteriors array to get Pr(AF>0) given that we can just compute 1.0 - array[0]. Integration tests change only because of trivial precision artifacts for reference calls using EMIT_ALL_SITES. Eric Banks 2011-12-18 00:31:47 -0500
  • 6dc52d42bf Implemented the proper QUAL calculation for multi-allelic calls. Integration tests pass except for the ones making multi-allelic calls (duh) and one of the SLOD tests (which used to print 0 when one of the LODs was NaN but now we just don't print the SB annotation for that record). Eric Banks 2011-12-18 00:01:42 -0500
  • 6059ca76e8 Removing cruft that snuck in last commit. Khalid Shakir 2011-12-16 23:00:16 -0500
  • 7486696c07 When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory. Updated various tests for above items and other small fixes. Khalid Shakir 2011-12-16 18:07:26 -0500
  • e5df9e0684 cleaner test output Mauricio Carneiro 2011-12-16 17:08:18 -0500
  • fcc21180e8 Added hardClipLeadingInsertions UnitTest for the ReadClipper Mauricio Carneiro 2011-12-16 17:22:40 -0500
  • 075be52adc Added hardClipByReferenceCoordinates (left and right tails) UnitTest for the ReadClipper Mauricio Carneiro 2011-12-16 17:05:46 -0500
  • 5bba44d693 Added hardClipByReferenceCoordinates UnitTest for the ReadClipper Mauricio Carneiro 2011-12-16 16:36:31 -0500
  • 5838ba529d Added hardClipByReadCoordinates UnitTest for the ReadClipper Mauricio Carneiro 2011-12-16 15:10:22 -0500
  • c26295919e Added hardClipBothEndsByReferenceCoordinates UnitTest for the ReadClipper Mauricio Carneiro 2011-12-16 14:36:27 -0500
  • 1994c3e3bc Only print warning about allele incompatibility when running there are genotypes in the file in CombineVariants Mark DePristo 2011-12-16 16:33:13 -0500
  • 1863da4d18 Spawn a more reasonable number of jobs in GATKPerformanceOverTime Mark DePristo 2011-12-16 16:14:07 -0500
  • b6067be952 Support for selecting only variants with specific IDs from a file in SelectVariants Mark DePristo 2011-12-16 16:10:18 -0500
  • d6d2f49c88 Don't print log if there are no BAMs Mark DePristo 2011-12-16 16:09:37 -0500
  • dbc2ed2887 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-16 15:12:22 -0500
  • 1179588475 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-16 15:11:59 -0500
  • 0e0d022e58 RandomForest.R now caches trees to disk to save cpu and storage costs Mark DePristo 2011-12-16 15:10:51 -0500
  • 78e0950a77 Minor bug fix for printing in SAMDataSource Mark DePristo 2011-12-16 11:45:40 -0500
  • 7bc0d18418 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-16 11:42:42 -0500
  • 5aa79dacfc Changing hidden optimization argument to advanced. Ryan Poplin 2011-12-16 10:29:20 -0500
  • 3642a73c07 Performance improvements for dynamically merging BAMs in read walkers. Matt Hanna 2011-12-16 09:37:44 -0500
  • 3414ecfe2e Restored serial version of reader initialization. Serial mode is default, as the performance gains aren't so huge. Mark DePristo 2011-12-16 09:07:40 -0500
  • fb1c9d2abc Restored serial version of reader initialization. Parallel mode is default. Mark DePristo 2011-12-16 09:05:28 -0500
  • 16a563889f GATKPerformance by default runs 10 iterations of each job Mark DePristo 2011-12-16 08:27:19 -0500
  • e61e5c7589 Refactor of ReadClipper unit tests Mauricio Carneiro 2011-12-15 13:09:46 -0500
  • 7c58d8e37d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-12-15 12:52:46 -0500
  • f38ed69fd0 Work around for a known adapter clipping issue. Temporary fix while adapter clipping is being rewritten. Ryan Poplin 2011-12-15 12:52:34 -0500
  • 4748ae0a14 Bugfix: Softclips before Hardclips weren't being accounted for Mauricio Carneiro 2011-12-14 19:17:49 -0500
  • 62a2e335bc Changing HardClipper contract to allow UNMAPPED reads Mauricio Carneiro 2011-12-15 11:08:19 -0500
  • 4b80e3c034 Support for VariantEval in GATK performance assessment Mark DePristo 2011-12-15 09:44:20 -0500
  • 7dc552c1d0 Now subsets down to jobs that actually ran, to avoid numeric problems in printing Mark DePristo 2011-12-15 09:03:10 -0500
  • 598a21d01c Adding new downsampling argument to haplotype caller qscript. Ryan Poplin 2011-12-15 08:49:21 -0500
  • 897d44abf9 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-15 08:45:33 -0500
  • 568d972991 Adding downsample per region argument to the haplotype caller Ryan Poplin 2011-12-15 08:43:48 -0500
  • 550fb498be Support for NT testing (default up to 4) for CC and UG Mark DePristo 2011-12-14 18:43:44 -0500
  • 9333b678b5 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-12-14 18:05:44 -0500
  • 6fb4be1a09 Cache header merger. Matt Hanna 2011-12-14 18:05:31 -0500
  • 9dbd0ef06a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-12-14 17:11:56 -0500
  • 3283d96bf2 Reducing the memory usage and runtime of the haplotype caller integration tests so that Eric can run them on his laptop. Ryan Poplin 2011-12-14 17:11:41 -0500
  • 50dee86d7f Added unit test to catch Ryan's exception Mauricio Carneiro 2011-12-14 16:52:43 -0500
  • 128bdf9c09 Create artificial reads with "default" parameters Mauricio Carneiro 2011-12-14 16:51:55 -0500
  • c85100ce9c Fix ClippingOp bug when performing multiple hardclip ops Mauricio Carneiro 2011-12-14 15:34:11 -0500
  • de5928ac5a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-14 16:24:56 -0500
  • 4fddac9f22 Updating busted integration tests Eric Banks 2011-12-14 16:24:43 -0500
  • 30e5531e1b GATKPerformanceOverTime includes CombineVariants, CountCovariates, TableRecalibrator, and SelectVariants Mark DePristo 2011-12-14 16:11:12 -0500
  • 01e547eed3 Parallel SAMDataSource initialization Mark DePristo 2011-12-14 10:00:21 -0500
  • 71b4bb12b7 Bug fix for incorrect logic in subsetSamples Mark DePristo 2011-12-14 09:58:23 -0500
  • 7ac8966184 G1K phased I table now includes calculation for chrX Mark DePristo 2011-12-14 16:13:15 -0500
  • e90d77e531 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-14 15:32:26 -0500
  • 35fc2e13c3 Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all. Eric Banks 2011-12-14 15:31:09 -0500
  • 1e90d602a4 Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles. Eric Banks 2011-12-14 13:38:20 -0500
  • 988d60091f Forgot to add in the new result class Eric Banks 2011-12-14 13:37:15 -0500
  • 4c077f9155 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-12-14 12:15:46 -0500
  • 08e0889f0a Adding multi sample haplotype caller integration test. Changing interval list to include multi-allelic event. Fix to force a consistent ordering of the best alleles so that the multi-allelic alleles and GLs come out in a deterministic order. Ryan Poplin 2011-12-14 12:15:30 -0500
  • 106bf13056 Use a thread local result object to collect the results of the exact calculation instead of passing in multiple pre-allocated arrays. Eric Banks 2011-12-14 12:05:50 -0500
  • 7648521718 Add check for mixed genotype so that we don't exception out for a valid record Eric Banks 2011-12-14 11:26:43 -0500
  • 9497e9492c Bug fix for complex records: do not ever reverse clip out a complete allele. Eric Banks 2011-12-14 11:21:28 -0500
  • 9740ae2090 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-14 10:43:59 -0500