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  • 944e1c299d Docs for --keepOriginalAC were wrong in SelectVariants Eric Banks 2012-08-22 13:07:13 -0400
  • 2409aa9bfd Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-22 12:54:43 -0400
  • 94540ccc27 Using the simple VCBuilder constructor and then subsequently trying to modify attributes was throwing a NPE. This is easily solved (without a performance hit) by initializing the attributes map to an immutable Collections.emptyMap(). Added unit test to cover this case. Eric Banks 2012-08-22 12:54:29 -0400
  • 901f47d8af Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still Guillermo del Angel 2012-08-22 11:38:51 -0400
  • 7df0abf49b Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-22 11:36:41 -0400
  • 9e76e8aa0b Just noticed that the efficient conversion to uppercase method is redundant since it's already implemented efficiently in Picard; let's just have a single implementation. Eric Banks 2012-08-22 11:26:08 -0400
  • 20601f034e Updating the checkType() function to include the new StructuralIndel variant type. Fixes outstanding broken integration test. Christopher Hartl 2012-08-22 07:33:10 -0700
  • c7ce3e1cf5 Merged bug fix from Stable into Unstable Eric Banks 2012-08-22 00:24:40 -0400
  • 03017855e4 WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test. Eric Banks 2012-08-22 00:24:01 -0400
  • 1acf18aa25 run_performance_tests use bsub and gsa Mark DePristo 2012-08-21 16:26:12 -0400
  • cb9ba4f660 Expand intervals processed for many GATKPerformanceOverTime commands Mark DePristo 2012-08-21 16:25:31 -0400
  • 1d707e7b31 Linear and Quadratic fits for GATKPerformanceOverTime.R Mark DePristo 2012-08-21 14:44:11 -0400
  • e43ff31eab GATKPerformance over time lives (mark II) Mark DePristo 2012-08-20 16:51:54 -0400
  • df36b4384c Update analyzeRunReports.py to handle new GATK tag argument Mark DePristo 2012-08-20 13:30:25 -0400
  • 6ce8016ae7 GSA-491: Add hidden tag to GATK that propagates to the GATK logs Mark DePristo 2012-08-20 13:19:35 -0400
  • 9eec33ec3b Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running Mark DePristo 2012-08-20 10:33:42 -0400
  • 6a8cf1c84a Enable and adapt HaplotypeScore and MappingQualityZero as active region annotations now that we have per-read likelihoods passed in to annotations Guillermo del Angel 2012-08-21 14:35:40 -0400
  • d0644b3565 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-21 10:35:23 -0400
  • 94e7f677ad Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-21 10:21:47 -0400
  • 418ace463a More merge conflict resolution Guillermo del Angel 2012-08-21 10:15:52 -0400
  • 10961db3ce Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous. Ryan Poplin 2012-08-21 09:35:55 -0400
  • 605acaae9c Another round of FindBugs fixes. Object internally stores a reference to an externally mutable array. Very dangerous. Ryan Poplin 2012-08-21 09:33:58 -0400
  • 55b7949d68 Another round of FindBugs fixes. Comparator doesn't implement Serializable. Ryan Poplin 2012-08-21 09:20:55 -0400
  • ba8622ff0d number of stashed changes are lurking in here. In order of importance: - Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker. - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length. - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR) - InsertSizeDistribution changed to use the new gatk report output (it was previously broken) - RetrogeneDiscovery changed to be compatible with the new gatk report - A maxIndelSize argument added to SelectVariants - ByTranscriptEvaluator rewritten for cleanliness - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; ) Christopher Hartl 2012-08-21 07:03:50 -0400
  • 3dfe8df262 Merged bug fix from Stable into Unstable Eric Banks 2012-08-20 23:12:58 -0400
  • 40d5efc804 Fix for Adam K's reported bug: we weren't handling reads that were entirely insertions properly in LIBS. Specifically, the event bases were off-by-one (which was disasterous in Adam's case with a 1bp read). Added a unit test to cover this case. Eric Banks 2012-08-20 23:12:41 -0400
  • 3514fb6e66 Changed the default memory limit from none to 2GB upon suggestions from delangel, carneiro, and depristo. Khalid Shakir 2012-08-20 21:39:38 -0400
  • 286b658fab Re-enabling parallelism in the BaseRecalibrator now that the release is out. Eric Banks 2012-08-20 21:25:14 -0400
  • 5b1781fdac Merge remote-tracking branch 'unstable/master' Eric Banks 2012-08-20 21:18:54 -0400
  • 7bbd2a7a20 Fixing merge conflicts Guillermo del Angel 2012-08-20 20:38:25 -0400
  • 2041cb853c New implementation of AD - ignore now non-informative reads based on per-read likelihoods Guillermo del Angel 2012-08-20 20:31:34 -0400
  • 77fbaec044 Another round of FindBugs fixes. Class implements its own compareTo() but uses base Object.equals() which can lead to unpredictable behavior. Ryan Poplin 2012-08-20 16:55:00 -0400
  • 5e28bca630 Another round of FindBugs fixes. Should be static inner class. Ryan Poplin 2012-08-20 16:15:48 -0400
  • a9472c1980 Another round of FindBugs fixes. Inefficient use of keySet iterator instead of entrySet iterator. Ryan Poplin 2012-08-20 16:11:45 -0400
  • 5db3bd6fd2 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-20 15:28:57 -0400
  • 464d49509a Pulling out common caller arguments into its own StandardCallerArgumentCollection base class so that every caller isn't exposed to the unused arguments from every other caller. Ryan Poplin 2012-08-20 15:28:39 -0400
  • 4450d66c64 Fixing the docs for DP and AD Eric Banks 2012-08-20 15:10:24 -0400
  • c67d708c51 Bug fix in HaplotypeCaller for non-regular bases in the reference or reads. Those events don't get created any more. Bug fix for advanced GenotypeFullActiveRegion mode: custom variant annotations created by the HC don't make sense when in this mode so don't try to calculate them. Ryan Poplin 2012-08-20 13:41:08 -0400
  • 5b5fee56cf Next iteration of new VA interface: extend changes to per-genotype annotations as well. Will allow to have AD correctly implemented at last (that change not done yet) Guillermo del Angel 2012-08-20 12:52:15 -0400
  • 154f65e0de Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons. Eric Banks 2012-08-20 12:43:17 -0400
  • 37dd7209df Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-08-20 12:31:34 -0400
  • c384677917 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-20 10:27:25 -0400
  • 97b191f578 Thanks to Guillermo I was able to isolate an instance of where the MLEAC > AN. It turns out that this is valid, e.g. when PLs are all 0s for a sample we no-call it but it's allowed to factor into the MLE (since that's the contract with the exact model). Removing the check in UG and instead protecting for it in the AlleleCount stratification. Eric Banks 2012-08-20 01:16:23 -0400
  • 963ad03f8b Second step of interface cleanup for variant annotator: several bug fixes, don't hash pileup elements to Maps because the hashCode() for a pileup element is not implemented and strange things can happen. Still several things to do, not done yet Guillermo del Angel 2012-08-19 21:18:18 -0400
  • 7fa76f719b Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info Mark DePristo 2012-08-19 10:32:55 -0400
  • 9121b98167 CombineVariants outputs the first non-MISSING qual, not the maximum Mark DePristo 2012-08-19 10:29:38 -0400
  • d9641e3d57 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-19 09:23:21 -0400
  • 342a5b68ed Bring bamboo performance test runner script under version control David Roazen 2012-08-18 21:06:57 -0400
  • d3206e35e0 Cleanup and expansion of GATKPerformanceOfTime Mark DePristo 2012-08-18 18:46:52 -0400
  • d16cb68539 Updated and more thorough version of the BadCigar read filter Mauricio Carneiro 2012-08-17 14:20:15 -0400
  • 980685af16 Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users. Mark DePristo 2012-08-17 14:55:17 -0400
  • 2676b7fc2e Put in a sanity check that MLEAC <= AN Eric Banks 2012-08-17 11:49:53 -0400
  • 0a706c9105 Add support for CombineVariants nt option in GATKPerformanceOverTime Mark DePristo 2012-08-17 11:48:43 -0400
  • bf6c0aaa57 Fix for missing formatter in R 2.15 Mark DePristo 2012-08-17 11:48:05 -0400
  • daa26cc64e Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance Mark DePristo 2012-08-17 11:41:07 -0400
  • be0f8beebb Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in. Mark DePristo 2012-08-17 11:21:49 -0400
  • a3d2764d11 Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings Mark DePristo 2012-08-17 10:35:25 -0400
  • 4c0f198d48 Potential fix for GSA-484: Incomplete writing of temp BCF when running CombineVariants in parallel Mark DePristo 2012-08-17 10:17:12 -0400
  • de3be45806 Proper function call in BCF2Decoder to validateReadBytes Mark DePristo 2012-08-17 10:14:19 -0400
  • 67ebd65512 Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts Mark DePristo 2012-08-17 10:13:40 -0400
  • 54e7302daf Improvements to GATKPerformanceOverTime Mark DePristo 2012-08-16 17:05:25 -0400
  • 53383e82ec Hmm, not good. Fixing the math in PBT resulted in changed MD5s for integration tests that look like significant changes. I am reverting and will report this to Laurent. Eric Banks 2012-08-16 21:41:18 -0400
  • 65c594afff Better error message for reads that begin/end with a deletion in LIBS Eric Banks 2012-08-16 21:27:07 -0400
  • b61ecc7c19 Fix merge conflicts Guillermo del Angel 2012-08-16 20:45:52 -0400
  • d26183e0ec First preliminary big refactoring of UG annotation engine. Goals: a) Remove gigantic hack that cached per-read haplotype likelihoods in a static array so that annotations would go back and retrieve them, b) unify interface for annotations between HaplotypeCaller and UnifiedGenotyper, c) as a consequence, removed and cleaned duplicated code. As a bonus, annotations have now more relevant info to help them compute values. Major idea is that per-read haplotype likelihoods are now stored in a single unified object of class PerReadAlleleLikelihoodMap. Class implementation in theory hides internal storage details from outside work (still may need work cleaning up interface), and this object(or rather, a Map from Sample->perReadAlleleLikelihoodMap) is produced by UGCalcLikelihoods. The genotype calculation is also able to potentially use this info if needed. All InfoFieldAnnotations now get an extra argument with this map. Currently, this map is only produced for indels in UG, or for all variants within HaplotypeCaller. If this map is absent (SNPs in UG), the old Pileup interface is used, but it's avoided whenever possible. FORMAT annotations are not yet changed but will be focus of second step. Major benefit will be that annotations will be able to very easily discard non-informative reads for certain events. HaplotypeCaller also uses this new class, and no longer hard-codes the mapping of allele ->list(reads) but instead uses the same objects and interfaces as the rest of the modules. Code still needs further testing/cleaning/reviewing/debugging Guillermo del Angel 2012-08-16 20:36:53 -0400
  • 6a2862e8bc GSA-483: Bug in GATKdocs for Enums Mark DePristo 2012-08-16 16:23:45 -0400
  • 3253fc216b FindBugs 'Maintainability' fixes Eric Banks 2012-08-16 15:53:06 -0400
  • 05cbf1c8c0 FindBugs 'Efficiency' fixes Eric Banks 2012-08-16 15:40:52 -0400
  • d8071c66ed Removing SlowGenotype object from GATK Mark DePristo 2012-08-16 15:22:10 -0400
  • a22e7a5358 Should've run 'ant clean' instead of just 'ant'. In any event, these are 2 cases where we are setting a class's internal static variable directly. Very dangerous. Eric Banks 2012-08-16 15:07:32 -0400
  • 47b4f7b7e5 One final FindBugs related fix. I think it's safe to consider these changes 'fixes' that are allowed to go in during a code freeze. Eric Banks 2012-08-16 14:59:05 -0400
  • ded0e11b45 Killing off some FindBugs 'Realiability' issues Eric Banks 2012-08-16 14:00:48 -0400
  • dac3958461 Killing off some FindBugs 'Usability' issues Eric Banks 2012-08-16 13:32:44 -0400
  • 611d9b61e2 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-16 13:05:36 -0400
  • 2df04dc48a Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests. Eric Banks 2012-08-16 13:05:17 -0400
  • 132cdfd9c1 GSA-488: MLEAC > AN error when running variant eval fixed Mark DePristo 2012-08-16 13:00:35 -0400
  • 4e42988c66 GSA-485: Remove repairVCFHeader from GATK codebase Mark DePristo 2012-08-16 12:39:54 -0400
  • 52bfe8db8a Make sure the storage writer is closed before running mergeInfo in multi-threaded output management Mark DePristo 2012-08-16 10:56:07 -0400
  • 7a247df922 Added -bcf argument to VCFWriter output to force BCF regardless of file extension Mark DePristo 2012-08-16 10:54:52 -0400
  • 28c8e3e6d7 Cleanup BCF2Codec Mark DePristo 2012-08-16 10:53:22 -0400
  • 9dc694b2e9 Meaningful error message and keeping tmp file when mergeInfo fails Mark DePristo 2012-08-16 10:01:10 -0400
  • a9a1c499fd Update md5 in VariantRecalibrationWalkers test for BCF2 -- only encoding differences Mark DePristo 2012-08-16 09:28:03 -0400
  • 04be0c92bf Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-08-15 23:13:32 -0400
  • 9035b554fb Adding tests for the --solid_nocall_strategy argument Eric Banks 2012-08-15 23:13:24 -0400
  • fa7605c643 Convert external.build.dir and external.dist.dir back to paths David Roazen 2012-08-15 22:54:13 -0400
  • f368e568db Implementing support in BaseRecalibrator for SOLiD no call strategies other than throwing an exception. For some reason we never transfered these capabilities into BQSRv2 earlier. Eric Banks 2012-08-15 22:52:56 -0400
  • 9d09230c26 Better docs for verbose output of Pileup Eric Banks 2012-08-15 21:55:08 -0400
  • 3556c36668 Disable general ploidy integration tests because they are running forever Mark DePristo 2012-08-15 21:12:55 -0400
  • c0a31b2e5b CombineVariants parallel integration tests Mark DePristo 2012-08-15 21:12:21 -0400
  • 669c43031a BCF2 optimizations; parallel CombineVariants Mark DePristo 2012-08-15 14:36:06 -0400
  • dafa7e3885 Temporarily disable StateMonitoringThreadTests while I get them reliably working across platforms Mark DePristo 2012-08-15 14:26:50 -0400
  • 2da82e27ac Autoscaling of memory requirements in GATKPerformanceOverTime Mark DePristo 2012-08-14 22:11:00 -0400
  • d70fd18900 Minor increase in tolerance to sum of states in UnitTest for StateMonitoringThreadFactory Mark DePristo 2012-08-14 22:10:42 -0400
  • ae4d4482ac Parallel combine variants! Mark DePristo 2012-08-14 22:10:07 -0400
  • bd7ed0d028 Enable efficient parallel output of BCF2 Mark DePristo 2012-08-14 22:08:49 -0400
  • 290fd33f3b GATKPerformanceOfTime.R updated to new script outputs Mark DePristo 2012-08-14 16:27:57 -0400
  • 9459e6203a Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates Mark DePristo 2012-08-14 16:27:30 -0400
  • be3230a1fd Initial implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates Mark DePristo 2012-08-14 15:02:45 -0400
  • fc1bd82011 GATK performance of time lives Mark DePristo 2012-08-14 08:39:28 -0400
  • f277d7c09e Removing parallelism bottleneck in the GATK Mark DePristo 2012-08-13 15:59:35 -0400