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  • 9464dfdbf2 Don't penalize the reduced reads for spanning deletions (when surrounding base quals are Q2s) Eric Banks 2012-09-24 14:06:07 -0400
  • f98b1d38b5 just lines indentation Ami Levy Moonshine 2012-09-24 13:47:09 -0400
  • 6a73265a06 RR bug: we were adding synthetic reads from the header only before the variant region, which meant that reads that overlap the variant region but that weren't used for the consensus (because e.g. of low base quality for the spanning base) were never being used at all. Instead, add synthetic reads from before and spanning the variant region. Eric Banks 2012-09-24 13:29:37 -0400
  • ef680e1e13 RR fix: push the header removal all the way into the inner loops so that we literally remove a read from the general header only if it was added to the polyploid header. Add comments. Eric Banks 2012-09-24 11:14:18 -0400
  • 1509153b4b Adding my little walker to assess reduced bam coverage against the original bam because it's turning out to be very useful. Eric Banks 2012-09-23 00:47:40 -0400
  • 0187f04a90 Proper fix for a previous RR bug fix: only remove reads from the header if they were actually used in the creation of the polyploid consensus. Eric Banks 2012-09-23 00:39:19 -0400
  • 74bb4e2739 Fixing the VariantContextUtilsUnitTest Eric Banks 2012-09-22 23:24:55 -0400
  • 344083051b Reverting the fix to the generalized ploidy exact model since it cannot handle it computationally. Will file this in the JIRA. Eric Banks 2012-09-22 23:07:28 -0400
  • 25e3ea879a Oops, missed this test before when updating md5s Eric Banks 2012-09-22 22:16:35 -0400
  • ced652b3dd RR bug: we need to call removeFromHeader() for reads that were used in creating a polyploid consensus or else they are reused later in creating synthetic reads. In the worst case, this bug caused the tool to create 2 copies of the reduced read. Eric Banks 2012-09-22 21:50:10 -0400
  • 60b93acf7d RR bug: we need to test that the mapping and base quals are >= the MIN values and not just >. This was causing us to drop Q20 bases. Eric Banks 2012-09-22 21:32:29 -0400
  • f6a22e5f50 ExperimentalReadShardBalancerUnitTest was being skipped; fixed David Roazen 2012-09-22 01:05:40 -0400
  • e077347cc2 Re-allow running the GATK with experimental downsampling David Roazen 2012-09-21 22:27:45 -0400
  • 34eed20aa6 PerSampleDownsamplingReadsIterator: fix for incorrect use of DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL David Roazen 2012-09-21 22:22:59 -0400
  • 133085469f Experimental, downsampler-friendly read shard balancer David Roazen 2012-09-12 13:00:29 -0400
  • ab8fa8f359 Bug fix: AlleleCount stratification in VariantEval didn't support higher ploidy and was producing bad tables Guillermo del Angel 2012-09-21 20:48:12 -0400
  • dcd31e654d Turn off RR tests while I debug Eric Banks 2012-09-21 17:26:00 -0400
  • 21251c29c2 Off-by-one error in sliding window manifests itself at end of a coverage region dropping the last covered base. Eric Banks 2012-09-21 17:22:30 -0400
  • 2c3dc291c0 Added positive/negative strand to the synthetic reads Mauricio Carneiro 2012-08-15 15:29:55 -0400
  • 51cb5098e4 Fixed the alignment issues with reads that started with empty consensus headers Mauricio Carneiro 2012-08-14 12:43:29 -0400
  • aa1d2f3a5b Not every consensus is well aligned. Need to check more, but starting position has been fixed. Mauricio Carneiro 2012-08-13 17:11:12 -0400
  • 97874b92d1 Program runs, but the consensus reads are all out of place and need more tags Mauricio Carneiro 2012-08-13 17:06:51 -0400
  • 3494a52ddc another intermediate commit to update changes from stable Mauricio Carneiro 2012-08-09 13:25:07 -0400
  • a89ff7b5dd Intermediate commit to resolve conflicts coming from stable Mauricio Carneiro 2012-08-08 15:50:55 -0400
  • 5d758bf97f Better run a shorter test -- should take 3 minutes total Mark DePristo 2012-09-20 18:54:14 -0400
  • d29218825d Fix grouping for display of GATKPerformanceOverTime Mark DePristo 2012-09-20 18:45:01 -0400
  • b5fa848255 Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output Mark DePristo 2012-09-20 18:44:32 -0400
  • 90b7df46cf Add invocation count and shorter timeout to NanoSchedulerUnitTest Mark DePristo 2012-09-20 17:36:47 -0400
  • ba9e95a8fe Revert "Reorganized NanoScheduler so that main thread does the reduces" Mark DePristo 2012-09-20 17:35:35 -0400
  • 7425ab9637 Reorganized NanoScheduler so that main thread does the reduces Mark DePristo 2012-09-20 17:07:49 -0400
  • 747694f7c2 Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-09-20 14:14:58 -0400
  • 1316b579f0 Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table. Eric Banks 2012-09-20 14:14:34 -0400
  • c492185be6 Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2012-09-20 12:56:07 -0400
  • d25579deeb A couple of minor things. Christopher Hartl 2012-09-20 12:48:13 -0400
  • 2e6f533996 Adding both unit and integration tests to cover the previous edge case of mismatched PLs Eric Banks 2012-09-20 11:55:28 -0400
  • 4b7edc72d1 Fixing edge case bug in the Exact model (both standard and generalized) where we could abort prematurely in the special case of multiple polymorphic alleles and samples with widely different depths of coverage (e.g. exome and low-pass). In these cases it was possible to call the site bi-allelic when in fact it was multi-allelic (but it wouldn't cause it to create a monomorphic call). Eric Banks 2012-09-20 10:59:42 -0400
  • ccb65a03e8 sorry, non-ASCII characters annoy some computers. Ryan Poplin 2012-09-20 10:14:48 -0400
  • 1ef6fa7eed QD and FS are doubles and select variants is more picky than variant filtration on that Mauricio Carneiro 2012-09-20 08:21:42 -0400
  • 4e160a267d quality control script for ReduceReads Mauricio Carneiro 2012-09-20 00:06:08 -0400
  • 087247f1f0 Allow longs and doubles in recalibration report to allow some backward compatibility Mark DePristo 2012-09-19 19:23:44 -0400
  • 2267b722b2 Proper error handling in NanoScheduler Mark DePristo 2012-09-19 16:59:24 -0400
  • 773af05980 Intermediate commit for proper error handling in the NanoScheduler Mark DePristo 2012-09-19 11:39:49 -0400
  • eb24dc920a GATKPerformanceOverTime now includes ideal scaling line by default Mark DePristo 2012-09-19 09:58:55 -0400
  • d2046b67b1 Remove problematic @Ensures from InputProducer. Mark DePristo 2012-09-19 09:58:36 -0400
  • 33fabb8180 Final V3 version of NanoScheduler Mark DePristo 2012-09-19 09:31:31 -0400
  • e18bc4e7b1 Adding PrintReads -baq and -bqsr to standard performance testing Mark DePristo 2012-09-19 08:22:20 -0400
  • 5734d756b5 Remove problematic @Invariant from EOFMarkedValue Mark DePristo 2012-09-18 19:47:19 -0400
  • aa9a1e8122 Warn GATK user if the number of requested threads > available processors on the machine Mark DePristo 2012-09-18 19:47:02 -0400
  • 76027d17e6 Add a few more UnitTests for InputProducer Mark DePristo 2012-09-13 15:32:28 -0400
  • 7605c6bcc4 Done GSA-515 Nanoscheduler / GSA-557 V3 nanoScheduler algorithm Mark DePristo 2012-09-13 12:50:03 -0400
  • 69e418c3f5 Intermediate commit for v3 NanoScheduling algorithm Mark DePristo 2012-09-12 10:18:52 -0400
  • c72db70416 Update downsample_to_coverage to 60 Joel Thibault 2012-09-19 16:19:17 -0400
  • ee31a54a03 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-09-19 16:09:45 -0400
  • 7cf9911924 Fixed ReduceReads bug where variant regions were missing. Mauricio Carneiro 2012-09-19 16:09:08 -0400
  • 26e35e5ee2 updating BQSR integration tests Ryan Poplin 2012-09-19 14:10:34 -0400
  • b99099f05c The BaseRecalibrator and DelocalizedBaseRecalibrator have gotten out of sync. Fixing. Ryan Poplin 2012-09-19 12:30:26 -0400
  • 7a7103a757 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-09-19 10:39:18 -0400
  • 0ea543e1fd Removing testing scaffolding from delocalized BQSR. The output recal table reports the data as doubles instead of integers. This changes the mapping-based BQSR integration tests. Final intermediate push before delocalized BQSR replaces previous BQSR. Ryan Poplin 2012-09-19 10:39:06 -0400
  • bebd5c14b8 Update general ploidy md5's due to bad merge of md5's in previous commit, and new shortened interval definition for EMIT_ALL_CONFIDENT_SITES was buggy Guillermo del Angel 2012-09-18 20:12:15 -0400
  • ccc3f4ff8d Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-09-17 09:58:27 -0400
  • ebf609f757 new R script for summmary tables of the pipeline Ami Levy Moonshine 2012-09-17 09:57:10 -0400
  • ee0b17d98f typo in VE Ami Levy Moonshine 2012-09-17 09:51:51 -0400
  • ca010160a9 Merge fix Guillermo del Angel 2012-09-14 14:05:21 -0400
  • 6b37350bc0 Two hairy bugs in pool caller: a) Site error model wasn't counting errors in insertions correctly - Alleles passed in had padded ref byte, but event base in PileupElement doesn't have it. As a result, mismatch rate was grossly overestimated with insertions and we missed several calls we should have made. Integration test reflects changes. b) Adding a ref GL to the exact model is correct mathematically but AFResult wasn't filled properly. As a result, QUAL was junk in pure ref sites, and in all other sites the last ref GL introduced wasn't properly updating Pr(AF>0). c) Added integration test that covers -out_mode EMIT_ALL_CONFIDENT_SITES. Not fully sure if the math is 100% correct (for both diploid and generalized case) but at least now diploid and non-diploid cases behave similarly. md5 of this new test will fail since it's taking me a long time to run so I'll update from Bamboo output shortly Guillermo del Angel 2012-09-14 13:13:22 -0400
  • f4ac92e95c Add clipping of the adaptor sequence to the delocalized BQSR. Ryan Poplin 2012-09-14 11:51:54 -0400
  • 3585f5375e Bug fix so that the delocalized BAQ GOP parameter is actually used by the BQSR. Ryan Poplin 2012-09-14 11:02:14 -0400
  • 86be50f18d Add note to docs that the --list argument requires full command-line Eric Banks 2012-09-14 10:58:44 -0400
  • 182344ad89 Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-09-12 23:56:44 -0400
  • 3d3578b1de Deal with empty Seq Menachem Fromer 2012-09-12 23:54:41 -0400
  • d380ef9956 revert 82b0bab5fbc4e57e0db30b0ec3d4676fccef40ba, bad idea Ryan Poplin 2012-09-12 15:42:29 -0400
  • e7200f1a40 adding verbose debug statements in BQSR Ryan Poplin 2012-09-12 15:40:07 -0400
  • 0206e09a6a Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-09-12 15:18:27 -0400
  • d94d0d15c2 Complete overhaul of previous commits to make it all work with scatter-gather. Now tracks output files correctly and can print to stdout. Eric Banks 2012-09-12 15:15:40 -0400
  • 699a7801b6 Force the in-walker BAQ calculation to use the new BAQGOP parameter. Ryan Poplin 2012-09-12 14:59:31 -0400
  • c9111bb23e Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-09-12 14:46:50 -0400
  • fafecf4ffd Adding BAQGOP parameter to the delocalized BQSR. Ryan Poplin 2012-09-12 14:46:18 -0400
  • bc1e03a6d8 Adding HC integration test for _structural_ insertions and deletions. Ryan Poplin 2012-09-12 12:25:39 -0400
  • faad2972d6 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-09-12 12:23:24 -0400
  • 849a2b8839 Adding HC integration test for _structural_ insertions and deletions. Ryan Poplin 2012-09-12 12:23:00 -0400
  • 4bb7a99f08 Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it. Eric Banks 2012-09-12 11:51:44 -0400
  • 994a4ff387 Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings). Eric Banks 2012-09-12 11:24:53 -0400
  • 96be1cbea9 My own integration test isn't passing with a clean checkout. This fix to the walker ought to do it. Christopher Hartl 2012-09-12 10:11:06 -0400
  • 546586b70e Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-09-12 10:09:42 -0400
  • bfbf1686cd Fixed nasty bug with defaulting to diploid no-call genotypes Mark DePristo 2012-09-12 07:08:03 -0400
  • d1ba17df5d Fixed nasty bug in BCF2 writer for case where all genotypes are missing Mark DePristo 2012-09-12 06:41:36 -0400
  • 91f3204534 VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself Mark DePristo 2012-09-11 16:52:54 -0400
  • d3bdb9c67e Choose queue based on assumed run time expectation Menachem Fromer 2012-09-12 03:36:57 -0400
  • 5764f1037c Added control of memory for matrix merging Menachem Fromer 2012-09-12 03:01:01 -0400
  • 625fb25eca Updated import Menachem Fromer 2012-09-12 02:17:24 -0400
  • 2ea28499e2 Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-09-12 01:58:53 -0400
  • 5cb08fd17c Added XHMM option to outputTargetsBySamples Menachem Fromer 2012-09-12 01:58:04 -0400
  • 5d19fca649 A couple of bug-fixy changes. 1) SelectVariants could throw a ReviewedStingException (one of the nasty "Bug:") ones if the user requested a sample that wasn't present in the VCF. The walker now checks for this in the initialize() phase, and throws a more informative error if the situation is detected. If the user simply wants to subset the VCF to all the samples requested that are actually present in the VCF, the --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES flag changes this UserException to a Warning, and does the appropriate subsetting. Added integration tests for this. Christopher Hartl 2012-09-11 23:01:00 -0400
  • 35d15278af Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-09-11 14:34:17 -0400
  • c23b794904 I find these per-readgroup plots to be useful. Not sure why there were turned off by default. Ryan Poplin 2012-09-11 14:31:59 -0400
  • 0dd745bb9b Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-09-11 11:01:41 -0400
  • 13831106d5 Fix GSA-535: storing likelihoods in allele map was busted when running HaplotypeCaller, only the last likelihood of a haplotype was being stored, as opposed to the max likelihood of all haplotypes mapping to an allele Guillermo del Angel 2012-09-11 11:01:26 -0400
  • 6fad0f25bb Merge Eric's LocusIteratorByStateUnitTest changes into LocusIteratorByStateExperimentalUnitTest David Roazen 2012-09-11 10:34:14 -0400
  • e25e617d1a Fixes GSA-515 Nanoscheduler GSA-560 / Fix display of NanoScheduler and MonitoringEfficiency Mark DePristo 2012-09-11 07:38:34 -0400
  • 64ee0a10fe Fix bad include in package.scala Mark DePristo 2012-09-10 16:40:15 -0400
  • d6e42d839c Fixes GSA-558 GATK ReadShards don't handle unmapped reads correctly. Mark DePristo 2012-09-10 16:39:49 -0400