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  • 0dc3d20d58 Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type Laurent Francioli 2011-11-16 09:33:13 +0100
  • 7d77fc51f5 Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type Laurent Francioli 2011-11-16 03:32:43 -0500
  • 0d163e3f52 SnpEff 2.0.4 support David Roazen 2011-11-15 16:05:20 -0500
  • df415da4ab More bug fixes on the way to passing all tests Mark DePristo 2011-11-15 17:38:12 -0500
  • 0be23aae4e Bugfixes on way to a working refactored VariantContext Mark DePristo 2011-11-15 17:20:14 -0500
  • 231c47c039 Bugfixes on way to a working refactored VariantContext Mark DePristo 2011-11-15 16:42:50 -0500
  • fb685f88ec Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Laurent Francioli 2011-11-15 16:23:53 -0500
  • 2b2514dad2 Moved many unused phasing walkers and utilities to archive Mark DePristo 2011-11-15 16:14:50 -0500
  • 460a51f473 ID field now stored in the VariantContext itself, not the attributes Mark DePristo 2011-11-15 14:56:33 -0500
  • 7fada320a9 The right fix for this test is just to delete it. Eric Banks 2011-11-15 14:53:27 -0500
  • 231b8e9f74 Do not output deletion only synthetic reads Mauricio Carneiro 2011-11-15 13:23:49 -0500
  • b45d10e6f1 The DP in the FORMAT field (per sample) must also use the representative count or else it's always 1 for reduced reads. Eric Banks 2011-11-15 10:23:59 -0500
  • 233e581828 Merging in Master Mark DePristo 2011-11-15 09:28:24 -0500
  • b66556f4a0 Update error message so that it's clear ReadPair Walkers are exceptions Eric Banks 2011-11-15 09:22:57 -0500
  • 6e1a86bc3e Bug fixes to VariantContext and GenotypeCollection Mark DePristo 2011-11-15 09:21:30 -0500
  • 284430d61d Added more basic UnitTests for ReadClipper Roger Zurawicki 2011-11-15 00:13:52 -0500
  • 8e91e19229 Merge branch 'master' of ssh://nickel/humgen/gsa-scr1/gsa-engineering/git/unstable Roger Zurawicki 2011-11-15 00:13:37 -0500
  • cde829899d compress Reduce Read counts bytes by offset Mauricio Carneiro 2011-11-14 18:07:41 -0500
  • a1ce3d8141 Not reporting counts to reduced deletions (temporary patch) Mauricio Carneiro 2011-11-14 13:52:36 -0500
  • 4ff8225d78 GenotypeMap -> GenotypeCollection part 3 Mark DePristo 2011-11-14 17:51:41 -0500
  • f0234ab67f GenotypeMap -> GenotypeCollection part 2 Mark DePristo 2011-11-14 17:42:55 -0500
  • ab0ee9b847 Perform only necessary validation in VariantContext modify methods David Roazen 2011-11-14 15:10:50 -0500
  • 2e9d5363e7 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-14 15:32:06 -0500
  • 1fbdcb4f43 GenotypeMap -> GenotypeCollection Mark DePristo 2011-11-14 15:32:03 -0500
  • 5c38a9cfd6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-11-14 15:00:03 -0500
  • f1db31f072 Attempt to reduce memory footprint of ValidationSiteSelector (if this doesn't work then a radical rewrite of the walker to make it two-pass will be necessary): don't log any attributes of original VCF, if we need chr counts later we can reannotate from original inputs. As things stand, we can't select SNP's genomewide due to memory usage. Guillermo del Angel 2011-11-14 14:56:09 -0500
  • 4dc9dbe890 One quick fix to previous commit Eric Banks 2011-11-14 14:42:12 -0500
  • b3313e1445 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-14 14:31:38 -0500
  • 7b2a7cfbe7 Transfer headers from the resource VCF when possible when using expressions. While there, VA was modified so that it didn't assume that the ID field was present in the VC's info map in preparation for Mark's upcoming changes. Eric Banks 2011-11-14 14:31:27 -0500
  • 9b5c79b49d Renamed InferredGeneticContext to CommonInfo Mark DePristo 2011-11-14 14:28:52 -0500
  • 077397cb4b Deleted MutableVariantContext Mark DePristo 2011-11-14 14:19:06 -0500
  • b11c535527 Deleted MutableGenotype Mark DePristo 2011-11-14 13:16:36 -0500
  • 509ecc62cc Another bug fix for when no samples are specified in ValidationSiteSelectionWalker Guillermo del Angel 2011-11-14 13:02:51 -0500
  • 79987d685c GenotypeMap contains a Map, not extends it Mark DePristo 2011-11-14 12:55:03 -0500
  • 7aee80cd3b Fix to deal with reduced reads containing a deletion Eric Banks 2011-11-14 12:23:46 -0500
  • 3d2970453b Misc minor cleanup Eric Banks 2011-11-14 09:41:54 -0500
  • 1347beef40 Merge branch 'PhaseByTransmission' Laurent Francioli 2011-11-14 11:31:28 +0100
  • 6881d4800c Added Integration tests for Phasing by Transmission Laurent Francioli 2011-11-14 10:47:51 +0100
  • 34acf8b978 Added Unit tests for new methods in GenotypeLikelihoods Laurent Francioli 2011-11-14 10:47:02 +0100
  • 1202a809cb Added Basic Unit Tests for ReadClipper Roger Zurawicki 2011-11-13 22:27:49 -0500
  • b7c33116af Minor docs update Eric Banks 2011-11-12 23:21:07 -0500
  • 76d357be40 Updating docs example to use -L since that's best practice Eric Banks 2011-11-12 23:20:05 -0500
  • af8e39c04d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-11-12 08:42:24 -0500
  • c95f015d77 a) Bug fix in validation site selector, b) Initial qscript for selection of random snps and indels for validation experiment Guillermo del Angel 2011-11-12 08:41:53 -0500
  • 8cd077f009 Writing a GATKReport table as output. Mauricio Carneiro 2011-11-11 18:52:33 -0500
  • fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects Mark DePristo 2011-11-11 15:00:35 -0500
  • cd3146f4cf Add hidden option to ValidationAmplicons to output slightly modified format to make file work with downstream SQNM tools more seamlessly at request of GAP: one line per record, keep probe identifier to 20 characters, no * in ref allele. Guillermo del Angel 2011-11-11 14:07:07 -0500
  • 40fbeafa37 VQSR will now detect if the negative model failed to converge properly because of having too few data points and automatically retry with more appropriate clustering parameters. Ryan Poplin 2011-11-11 11:52:30 -0500
  • 4938569b3a More general handling of parameters for VariantContextBenchmark Mark DePristo 2011-11-11 10:22:19 -0500
  • ef9f8b5d46 Added subContextOfSamples to VariantContext Mark DePristo 2011-11-11 10:07:11 -0500
  • e216e85465 First working version of VariantContextBenchmark Mark DePristo 2011-11-11 09:56:00 -0500
  • ee40791776 Attributes are now Map<String,Object> not Map<String,?> Mark DePristo 2011-11-11 09:55:42 -0500
  • 59945a41e8 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-10 23:05:20 -0500
  • 0c32281484 Adding a benchmarking class for parsing VCF files. Not complete. Eric Banks 2011-11-10 23:05:13 -0500
  • 9c013374fd A walker to calculate the coverage of a target Mauricio Carneiro 2011-11-10 16:32:25 -0500
  • ffa6bc66ec Eliminating excessive debug tests Mauricio Carneiro 2011-11-10 14:32:21 -0500
  • 5a1170078a Using centralized reduce read facilities Mauricio Carneiro 2011-11-10 14:19:29 -0500
  • dc9b351b5e Meaningful error message when an IntervalArg file fails to parse correctly Mark DePristo 2011-11-10 17:10:26 -0500
  • bb7bf74aa8 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-10 16:05:43 -0500
  • 153e52ffed VariantEvalIntegrationTest for IntervalStratification Mark DePristo 2011-11-10 14:10:39 -0500
  • 060c7ce8ae It wouldn't harm integrationtests if we had our logic right... :-) Mauricio Carneiro 2011-11-10 14:03:22 -0500
  • bb4cd59475 Filtered and consensus reads will now use the same tag Mauricio Carneiro 2011-11-10 13:37:02 -0500
  • 7a46273d75 Consensus reads had filtered data read names Mauricio Carneiro 2011-11-10 12:56:29 -0500
  • c14b182501 Add reads in the recursive call Mauricio Carneiro 2011-11-10 12:29:10 -0500
  • 07dbf0bd40 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-11-10 13:39:24 -0500
  • 26762d6c6f Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC. Ryan Poplin 2011-11-10 13:36:03 -0500
  • 39678b6a20 Check for reads with missing read groups and throw a UserException when encountered. Mauricio said this wouldn't break integration tests. Eric Banks 2011-11-10 13:34:03 -0500
  • 18f829f76b Towards a full G1KPhaseI table creation script Mark DePristo 2011-11-10 13:27:54 -0500
  • dd1810140f -stratIntervals is optional Mark DePristo 2011-11-10 13:27:32 -0500
  • 67b022c34b Cleanup for new SampleUtils function Mark DePristo 2011-11-10 13:27:13 -0500
  • 9490d71bc8 Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC. Ryan Poplin 2011-11-10 13:26:29 -0500
  • 35fe9c8a06 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-10 11:11:33 -0500
  • 714cac21c9 Testdata for IntervalStratification Mark DePristo 2011-11-10 11:08:34 -0500
  • dc4932f93d VariantEval module to stratify the variants by whether they overlap an interval set Mark DePristo 2011-11-10 10:58:40 -0500
  • 0d8983feee outputting the RG information Mauricio Carneiro 2011-11-09 23:34:29 -0500
  • 315ac68b0b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-09 22:37:36 -0500
  • 6313aae2c4 Adding checks for hasBasePileup() before calling getBasePileup() as per GS thread Eric Banks 2011-11-09 22:37:26 -0500
  • 74a18d3de8 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-11-09 22:29:40 -0500
  • 24712c0221 Merged bug fix from Stable into Unstable Ryan Poplin 2011-11-09 22:28:27 -0500
  • 8942406aa2 Use MathUtils to compare doubles instead of testing for equality Ryan Poplin 2011-11-09 22:05:21 -0500
  • 348f2db7fd Fix for HMM optimization. If the two penalty arrays match exactly the function should return the end of the array instead of 0. Ryan Poplin 2011-11-09 22:00:52 -0500
  • 9a4486a9e6 BaseCounts now include N's Mauricio Carneiro 2011-11-09 21:29:33 -0500
  • 82bf09edf3 Mark Standard Annotations with an asterisk Eric Banks 2011-11-09 20:42:31 -0500
  • 04b122be29 Fix for bug reported on GetSatisfaction Eric Banks 2011-11-09 20:33:36 -0500
  • d00b2c6599 Adding a synthetic read for filtered data Mauricio Carneiro 2011-11-09 20:09:12 -0500
  • 3afbd0e526 Sliding Window Header now includes filtered data information Mauricio Carneiro 2011-11-09 17:04:18 -0500
  • 6ee90ada14 Quick optimization to the SlidingWindow builder Mauricio Carneiro 2011-11-09 15:30:17 -0500
  • 21bf43f3bb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-09 15:34:40 -0500
  • 02d5e3025e Added integration test for intervals from bed file Eric Banks 2011-11-09 15:34:19 -0500
  • 85bffe1dca Merged bug fix from Stable into Unstable Christopher Hartl 2011-11-09 15:29:14 -0500
  • d828eba7f4 Allow comments in a table-formatted file to precede the header line. Christopher Hartl 2011-11-09 15:27:38 -0500
  • 8205efbb29 Merge branch 'master' into intervals Eric Banks 2011-11-09 15:27:15 -0500
  • d64f8a89a9 Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly. Eric Banks 2011-11-09 15:24:29 -0500
  • 0111e58d4e Don't generate PDF unless you have -run specified Mark DePristo 2011-11-09 14:45:40 -0500
  • 29df96a77b First working version of G1KPhase1SummaryTable.scala Mark DePristo 2011-11-09 14:43:53 -0500
  • f080f64f99 Preserve RG information on new GATKSAMRecord from SAMRecord Mauricio Carneiro 2011-11-09 12:46:27 -0500
  • f9530e0768 Clean unnecessary attributes from the read Mauricio Carneiro 2011-11-09 12:37:14 -0500
  • 9427ada498 Fixing no cigar bug Mauricio Carneiro 2011-11-09 12:15:54 -0500
  • e639f0798e mergeEvals allows you to treat -eval 1.vcf -eval 2.vcf as a single call set Mark DePristo 2011-11-09 14:35:50 -0500
  • 149b79eaad Merged bug fix from Stable into Unstable Christopher Hartl 2011-11-09 11:26:30 -0500