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  • 9604fb2ba3 Necessary but not sufficient step to fix GenotypeGivenAlleles mode in UG which is now busted Guillermo del Angel 2011-09-07 16:49:16 -0400
  • 2ded027762 Removed dysfunctional tranches support from VariantEval Mark DePristo 2011-09-07 16:09:24 -0400
  • aa9e32f2f1 Reverting Mark's previous commit as per the open discussion. Now the eval modules check isPolymorphic() before accruing stats when appropriate. Fixed the IndelLengthHistogram module not to error out if the indel isn't simple (that would have been bad). Only integration test that needed to be updated was the tranches one based on a separate commit from Mark. Eric Banks 2011-09-07 15:48:06 -0400
  • d7e355b4b6 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-07 14:54:16 -0400
  • 9127849f5d BugFix for unit test Mark DePristo 2011-09-07 14:54:10 -0400
  • 0037b61e5d Class of scala file should be close to filename, not MDP Mark DePristo 2011-09-07 14:48:54 -0400
  • 3a04955a30 We already had isPolymorphic and isMonomorphic in the VariantContext, but the implementation was incorrect for many edge cases (e.g. sites-only files, sites with samples who were no-called). Fixing. Moving on to VE now. Eric Banks 2011-09-07 14:01:42 -0400
  • ee9d599558 Just cleaning up Mauricio Carneiro 2011-09-07 13:31:20 -0400
  • 743bf7784c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-09-07 13:21:26 -0400
  • 5f22ef9a8c Added missing javadoc info to Beagle arguments Guillermo del Angel 2011-09-07 13:21:11 -0400
  • 3bcbfa6e06 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-07 13:13:17 -0400
  • 430da23446 At least 2 minutes must pass before a status message is printed, further stabilizing time estimates Mark DePristo 2011-09-07 13:13:07 -0400
  • 6857d0324e Merge branch 'master' into rr Mauricio Carneiro 2011-09-07 12:59:08 -0400
  • 7e9e20fed0 Forgot to delete previous call Mark DePristo 2011-09-07 12:54:52 -0400
  • d23d620494 Pushing traversal engine timer start to as close to actual start as possible Mark DePristo 2011-09-07 12:52:33 -0400
  • 6ff432e1f2 BugFix for TF argument to VariantEval, actually making it work properly Mark DePristo 2011-09-07 12:50:17 -0400
  • 131cb7effd Bringing Reduce Reads bug fixes to the main repository Mauricio Carneiro 2011-09-07 12:25:53 -0400
  • a1920397e8 Major bugfix for per sample VariantEval Mark DePristo 2011-09-07 12:18:11 -0400
  • a02636a1ac Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/ebanks/Sting_rodrefactor into rodrewrite Mark DePristo 2011-09-07 10:50:00 -0400
  • d5641cfac5 Merge branch 'variantEvalST' Mark DePristo 2011-09-07 10:44:23 -0400
  • 2f4cf82e3b VariantEval cleanup. Added VariantType Stratification Mark DePristo 2011-09-07 10:43:53 -0400
  • 436f6eb52b Reverting Eric's change and pushing in some command-line-option documentation. Christopher Hartl 2011-09-07 08:53:30 -0400
  • 1ef8a1750a I asked nicely and got nothing. Then I threatened and still got nothing. So I am carrying through on my threats. Guillermo, you have a short reprieve because you were away on vacation, but let's get yours done tomorrow afternoon. Eric Banks 2011-09-06 21:07:49 -0400
  • da9c8ab386 Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly. Eric Banks 2011-09-06 20:39:42 -0400
  • 9559115ad5 Bugfix for singleton runs. Now with histograms where possible Mark DePristo 2011-09-06 16:54:01 -0400
  • 388d377677 Merge branch 'rrOpt' Mark DePristo 2011-09-06 15:11:49 -0400
  • 3db7ecb920 ReducedRead flag cached in GATKSAMRecord. 20% performance improvement Mark DePristo 2011-09-06 15:09:37 -0400
  • 2d5509e8a6 Now includes the RQ flag in the consensus reads Mark DePristo 2011-09-06 14:42:27 -0400
  • 284f83469b ReducedRead flag cached in GATKSAMRecord. 20% performance improvement Mark DePristo 2011-09-06 15:09:37 -0400
  • f3ab7d7c0d Now includes the RQ flag in the consensus reads Mark DePristo 2011-09-06 14:42:27 -0400
  • 47607a7eff Fixed bug where deletions messed up interval clipping Roger Zurawicki 2011-09-06 14:25:57 -0400
  • b0b803aa00 Fix for default value of maximum_consensus_base_qual, which can be at most 94 Mark DePristo 2011-09-06 14:12:54 -0400
  • 0adb388dee Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue. Updates for HybridSelectionPipeline: - Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5. - If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds. - Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches. - Removed GSA_PRODUCTION_ONLY flag from indel caller. - Updated indel hard filters based on delangel's analysis. - Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now. Khalid Shakir 2011-09-06 12:41:46 -0400
  • d471617c65 GATK binary VCF (gvcf) prototype format for efficiency testing Mark DePristo 2011-09-02 21:15:19 -0400
  • 048202d18e Bugfix for cached quals Mark DePristo 2011-09-02 21:13:28 -0400
  • 03aa04e37c Simple refactoring to make formating functions public Mark DePristo 2011-09-02 21:13:08 -0400
  • 124ef6c483 MISSING_VALUE now gets defaultValue in getAttribute functions Mark DePristo 2011-09-02 21:12:28 -0400
  • 28d782b4c7 Allowing multiple dnsnp and indel files in the DPP Mauricio Carneiro 2011-09-02 13:38:35 -0400
  • 8da36a965e Moving the ReadClipping further upstream into the HaplotypeCaller Ryan Poplin 2011-09-02 13:27:47 -0400
  • 82f2131777 Simplied getAttributeAsX interfaces Mark DePristo 2011-09-02 12:27:11 -0400
  • 08ae6c0c61 ReadClipper is now handling unmapped reads Mauricio Carneiro 2011-09-02 11:32:30 -0400
  • c57198a1b9 Optimizations in VCFCodec Mark DePristo 2011-09-02 08:46:17 -0400
  • c3ea96d856 Removing many unused functions of unquestionable purpose Mark DePristo 2011-09-02 08:42:01 -0400
  • d241f0e903 Adding docs for the pcr error rate argument. Eric Banks 2011-09-01 21:57:02 -0400
  • ad4ea0b80b Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-09-01 18:14:45 -0400
  • e253f6f05d Fixing typo in DPP Mauricio Carneiro 2011-09-01 18:13:52 -0400
  • d2a33beff7 Added WGS/WEX b37-decoy CEU trio datasets Mauricio Carneiro 2011-09-01 13:14:40 -0400
  • 827fe6130c Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one). Eric Banks 2011-09-01 11:40:35 -0400
  • 0b794b5491 Reving Tribble to 23 Mark DePristo 2011-09-01 10:43:03 -0400
  • 1aa4b12ff0 Reduced the number of combinations being tested here, which was overkill Mark DePristo 2011-09-01 10:42:43 -0400
  • ac49b8d26b Conditional support for PerformanceTrackingQuerySource to measure Tribble / GATK bridge performance Mark DePristo 2011-09-01 10:41:55 -0400
  • 2b97017871 Fix @Output that should be @Argument Mark DePristo 2011-09-01 10:37:20 -0400
  • a522488121 First pass at using the indel realigner code to realign reads to the newly assembled haplotypes. Misc bug fix in genotyping engine when both haplotype's alt alleles were deletions. Ryan Poplin 2011-09-01 09:55:30 -0400
  • 8529075e60 misc cleanup Ryan Poplin 2011-08-31 18:53:41 -0400
  • 70a1ba6fa1 Using ReadClipper to clip the reads instead of manually looking for strings of consecutive high quality bases Ryan Poplin 2011-08-31 18:52:08 -0400
  • f57547ad63 Enabling soft clipped bases in the assembly engine of the haplotype caller Ryan Poplin 2011-08-31 18:21:56 -0400
  • dd89755e74 Merged bug fix from Stable into Unstable Matt Hanna 2011-08-31 17:28:44 -0400
  • 65a9159ac6 Point ivy to the maven repo instead of the default ibiblio repo. Drastically simplify ivy config by completely cutting out module specifications. Matt Hanna 2011-08-31 17:27:25 -0400
  • 4b5a7046c5 Making ReadLengthDistribution Public Mauricio Carneiro 2011-08-31 15:34:58 -0400
  • d604019362 Finished my broken tribble code. Updated to rev 22 Mark DePristo 2011-08-30 16:56:48 -0400
  • 2585728f03 Fixing the build David Roazen 2011-08-30 12:45:53 -0400
  • bdf04b8057 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-30 11:08:23 -0400
  • 173ca1e215 Reverting tribble temporarily while I fix my subtle problems Mark DePristo 2011-08-30 11:08:13 -0400
  • e040ea5c0d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-30 08:34:01 -0400
  • 60582215be Upping the kmer length in order to see larger events Ryan Poplin 2011-08-30 08:33:49 -0400
  • 7d79de91c5 Merge branch 'master' into rr Mauricio Carneiro 2011-08-30 02:50:19 -0400
  • 0cd9438ac2 fixed soft unclipped calculation Mauricio Carneiro 2011-08-30 02:31:00 -0400
  • 39d8dccc9c Don't close an empty sliding window Mauricio Carneiro 2011-08-29 18:42:12 -0400
  • fd540592ab Added RMS calculation for consensus MQ Mauricio Carneiro 2011-08-29 18:15:26 -0400
  • 7271998735 Ignore insertions at the beginning of a read. Mauricio Carneiro 2011-08-29 17:52:37 -0400
  • f2cc483c22 Adding mapping quality filter to consensus Mauricio Carneiro 2011-08-29 17:51:02 -0400
  • b2f39fef8e don't output deletions as bases in the read (consensus) Mauricio Carneiro 2011-08-29 16:21:21 -0400
  • dc140b9f18 Fixed window header construction for out of order reads Mauricio Carneiro 2011-08-29 13:03:56 -0400
  • 6f9264d2b3 Hard Clipping no longer leaves indels on the tails Mauricio Carneiro 2011-08-29 01:51:57 -0400
  • 943876c6eb Added QUAL/MINVAR parameters to the walker Mauricio Carneiro 2011-08-28 19:25:35 -0400
  • c81675be4c Never allow deletions in the consensus Mauricio Carneiro 2011-08-28 17:04:44 -0400
  • 7532be7f5a Allowing to clip after AlignmentEnd if end is soft clipped. Mauricio Carneiro 2011-08-28 16:06:41 -0400
  • 90a1f5e15c Several bug fixes Mauricio Carneiro 2011-08-28 01:47:03 -0400
  • 66a8b36cf5 Fixed most indexing bugs Mauricio Carneiro 2011-08-27 23:25:26 -0400
  • 6a4a47568c Added sample script for generating per sample metrics and updated the queue.sh used for running pipelines to be renamed. Khalid Shakir 2011-08-29 22:10:35 -0400
  • 077b6a58da Merging (un-merging?) reverts into unstable. Current unstable uses "leftAligned" while current stable does not use "leftAligned". Khalid Shakir 2011-08-29 20:09:48 -0400
  • 5fdd10340a Merged bug fix from Stable into Unstable Khalid Shakir 2011-08-29 20:08:04 -0400
  • cf2430322a Manually fixing unintentional path changes for dbsnps. Khalid Shakir 2011-08-29 20:06:28 -0400
  • 2125ba1f23 Merged bug fix from Stable into Unstable Khalid Shakir 2011-08-29 19:36:43 -0400
  • 20ac24464d Rev'ved picard to read new analysis_files.txt with a blank line after header and no reference sequence. Updated error messages and unit tests. Khalid Shakir 2011-08-29 19:33:04 -0400
  • 427c643ce7 The missing tribble jar Mark DePristo 2011-08-29 18:46:40 -0400
  • c6d8df8639 queueJobReport is a public feature of Queue Mark DePristo 2011-08-29 17:20:54 -0400
  • 1e5001b447 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-29 17:04:21 -0400
  • 5defaf5fac Continuing to improve Tribble Mark DePristo 2011-08-29 17:02:57 -0400
  • 3af001fff2 Bugfix for file that must not exist on disk Mark DePristo 2011-08-29 17:00:10 -0400
  • 71680e3fd6 Extremely minor tweaks to the GSAPipelineIndexer David Roazen 2011-08-29 16:50:38 -0400
  • 3b09d42ed6 Now only prints 1 warning message about duplicate headers in simpleMerge Mark DePristo 2011-08-29 14:41:29 -0400
  • c2f0db969b Don't use the default deletion value from UG if not asking to have it set Eric Banks 2011-08-29 13:48:10 -0400
  • bb7a37e8f2 We need to allow reference calls in the input VCF for the GenotypeAndValidate walker when using the BAM as truth so that we can test supposed monomorphic calls against the truth. Eric Banks 2011-08-29 13:19:35 -0400
  • 5b56c83401 Don't output variants that on the edges of the haplotype, far away from the original interval. Ryan Poplin 2011-08-29 11:15:07 -0400
  • 661d658a0e Updating smith-waterman parameters for the general case of aligning both with indels and snps simultaneously Ryan Poplin 2011-08-29 09:49:34 -0400
  • bc252a0d62 misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR Ryan Poplin 2011-08-29 08:11:31 -0400
  • f9afc5876a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-29 08:04:39 -0400
  • 61633c95a8 Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt Mark DePristo 2011-08-28 19:19:45 -0400
  • a5c65fc133 Debugging information to print out the Query tracks Mark DePristo 2011-08-28 18:54:49 -0400