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  • 09a5a9eac0 Don't update lineNo for decodeLoc - only for decode (otherwise they get double-counted). Even still, because of the way the GATK currently utilizes Tribble we can parse the same line multiple times, which knocks the line counter out of sync. For now, I've added a TODO in the code to remind us and the error messages note that it's an approximate line number. Eric Banks 2011-12-14 10:43:52 -0500
  • d3f4a5a901 Fail gracefully when encountering malformed VCFs without enough data columns Eric Banks 2011-12-14 10:37:38 -0500
  • e061e236ab Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-12-14 10:24:48 -0500
  • 23f15851c1 Turn off haplotype caller verbose debug output by default. Ryan Poplin 2011-12-14 10:24:33 -0500
  • 079932ba2a The log10cache needs to be larger if we want to handle 10K samples in the UG. Eric Banks 2011-12-13 23:36:10 -0500
  • 6d6bed1ccc Linear time ROC calculation Mark DePristo 2011-12-13 18:46:16 -0500
  • 7dd5c74591 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-13 18:19:41 -0500
  • ebbdd02569 V1 of random forest analysis script Mark DePristo 2011-12-13 18:19:16 -0500
  • cd390277d0 Adding temporary read filter to HaplotypeCaller integration test while ReadClipper contracts are being worked out. Ryan Poplin 2011-12-13 17:41:10 -0500
  • 7fa1ab1bae Fix to allow haplotype caller to call indels after UG engine entry points were unified. Adding Haplotype Caller integration test Ryan Poplin 2011-12-13 17:19:40 -0500
  • 7a386b45a5 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-12-13 15:59:52 -0500
  • 32a1e729ba Bug fix in HaplotypeCaller for multiallelics with SNP and indel starting at same locus Ryan Poplin 2011-12-13 15:59:43 -0500
  • e47a113c9f Enabled multi-allelic SNP discovery in the UG. Needs loads of testing so do not use yet. While working in the UG engine, I removed the extraneous and unnecessary MultiallelicGenotypeLikelihoods class: now a VariantContext with PL-annotated Genotypes is passed around instead. Integration tests pass so it must all work, right? Eric Banks 2011-12-12 23:02:45 -0500
  • 5cc1e72fdb Parallelized SelectVariants Mauricio Carneiro 2011-12-12 18:41:04 -0500
  • 663184ee9d Added test mode to PPP Mauricio Carneiro 2011-12-12 18:08:29 -0500
  • a3c3d72313 Added test mode to DPP Mauricio Carneiro 2011-12-12 12:35:36 -0500
  • a70a0f25fb Better debug output for SAMDataSource Mauricio Carneiro 2011-12-12 17:55:39 -0500
  • 1ba1717ad8 Queue framework to compute UG, CountLoci and other walkers performance across GATK versions Mark DePristo 2011-12-12 17:32:26 -0500
  • d03425df2f TODO optimization targets Mark DePristo 2011-12-12 14:46:45 -0500
  • 3519a897c4 Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-12-12 11:00:47 -0500
  • c8b1c92a6c Updating the other half of the PPP Mauricio Carneiro 2011-12-12 10:55:41 -0500
  • 2a32ebe104 Bringing Laurent's Mendelian Violation changes to the main repo -- he promised to follow the guidelines next time Mauricio Carneiro 2011-12-12 09:52:08 -0500
  • 1008c453ec Merge remote-tracking branch 'lau/master' into laurent Mauricio Carneiro 2011-12-12 09:50:58 -0500
  • 52c64b971f Updating MD5s -- really dont know why it didn't update before Mauricio Carneiro 2011-12-12 09:48:58 -0500
  • 7cf27bb66e Updated md5sum for MendelianViolationEvaluator test to reflect the change in column alignment in VariantEval. Laurent Francioli 2011-12-12 12:22:43 +0100
  • 025bdfe2cc Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Laurent Francioli 2011-12-12 12:19:44 +0100
  • ed91461c49 Data Processing Pipeline Test Mauricio Carneiro 2011-12-12 00:24:51 -0500
  • cca8a18608 PPP pipeline test Mauricio Carneiro 2011-12-11 13:16:23 -0500
  • 019dbd083d Exploratory walker to calculate fraction-based equivalences from Yamagishi Mark DePristo 2011-12-11 17:31:25 -0500
  • 7b6338c742 Merge branch 'master' into trialleles Eric Banks 2011-12-11 00:28:46 -0500
  • 7c4b9338ad The old bi-allelic implementation of the Exact model has been completely deprecated - you can only use the multi-allelic implementation now. Eric Banks 2011-12-11 00:23:33 -0500
  • 044f211a30 Don't collapse likelihoods over all alt alleles - that's just not right. For now, the QUAL is calculated for just the most likely of the alt alleles; I need to think about the right way to handle this properly. Eric Banks 2011-12-10 23:57:14 -0500
  • 21ac3b59d7 Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-12-09 16:51:46 -0500
  • 13905c00b3 Updating PacbioProcessingPipeline to new Queue standards Mauricio Carneiro 2011-12-09 16:51:02 -0500
  • 364f1a030b Plumbing added so that the UG engine can handle multiple alleles and they can successfully be genotyped. Alleles that aren't likely are not allowed to be used when assigning genotypes, but otherwise the greedy PL-based approach is what is used. Moved assign genotypes code to UG engine since it has nothing to do with the Exact model. Still have some TODOs in here before I can push this out to everyone. Eric Banks 2011-12-09 14:25:28 -0500
  • 8475328b2c Turning off test that breaks read clipper Mauricio Carneiro 2011-12-09 11:53:12 -0500
  • 4cbd1f0dec Reorganized the testing code and created ClipReadsTestUtils Roger Zurawicki 2011-11-29 18:30:23 -0500
  • 0e9c2cefa2 testHardClipSoftClippedBases works with Matches and Deletions Roger Zurawicki 2011-11-23 06:42:03 -0500
  • 64dad13e2d Don't carry around an extra copy of the code for the Haplotype Caller Eric Banks 2011-12-09 11:09:40 -0500
  • 442ceb6ad9 The Exact model now computes both the likelihoods and posteriors (in separate arrays); likelihoods are used for assigning genotypes, not the posteriors. Eric Banks 2011-12-09 10:16:44 -0500
  • a79144f7db Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Laurent Francioli 2011-12-09 15:57:24 +0100
  • 72fbfba97d Added UnitTests for getFamilies() and getChildrenWithParents() Laurent Francioli 2011-12-09 15:57:07 +0100
  • 5a06170804 Corrected bug causing getChildrenWithParents() to not take the last family member into consideration. Laurent Francioli 2011-12-09 14:51:34 +0100
  • 6a4102f23a Merge remote-tracking branch 'lau/master' into laurent Mauricio Carneiro 2011-12-09 07:06:52 -0500
  • aa4a8c5303 No dynamic programming solution for assignning genotypes; just done greedily now. Fixed QualByDepth to skip no-call genotypes. No-calls are no longer given annotations (attributes). Eric Banks 2011-12-09 02:25:06 -0500
  • 2fe50c64da Updating md5s Eric Banks 2011-12-09 00:47:01 -0500
  • 8777288a9f Don't throw a UserException if too many alt alleles are trying to be genotyped. Instead, I've added an argument that allows the user to set the max number of alt alleles to genotype and the UG warns and skips any sites with more than that number. Eric Banks 2011-12-09 00:00:20 -0500
  • 3e7714629f Scrapped the whole idea of an int/long as an index into the ACset: with lots of alternate alleles we run into overflow issues. Instead, simply use the ACcounts array as the hash key since it is unique for each AC conformation. To do this, it needed to be wrapped inside an object so hashcode() would work. Eric Banks 2011-12-08 23:50:54 -0500
  • 4aebe99445 Need to use longs for the set index (because we can run out of ints when there are too many alternate alleles). Integration tests now use the multiallelic implementation. Eric Banks 2011-12-08 15:31:02 -0500
  • 7750bafb12 Fixed bug where last dependent set index wasn't properly being transferred for sites with many alleles. Adding debugging output. Eric Banks 2011-12-08 13:50:50 -0500
  • 252e0f3d0a Merged bug fix from Stable into Unstable Guillermo del Angel 2011-12-08 13:11:39 -0500
  • 1bfe28067f Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc. Guillermo del Angel 2011-12-08 12:54:08 -0500
  • 50c4436f90 scales=free shows variance within analysis better Mark DePristo 2011-12-07 14:09:32 -0500
  • 9def841275 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-07 13:36:16 -0500
  • 69b19047ba Fix bad path Mark DePristo 2011-12-07 12:08:25 -0500
  • 4055877708 Prints 0.0 TiTv not NaN when there are no variants Mark DePristo 2011-12-07 12:07:54 -0500
  • 44bc8766d7 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-12-07 12:03:27 -0500
  • 15533e08df Fixed issue with RODWalker parallelization. Matt Hanna 2011-12-07 11:55:42 -0500
  • 831010e72f Misc minor updates and added comments to the HaplotypeCaller. Merging branches in prep for work on active region traversal. Ryan Poplin 2011-12-07 10:08:29 -0500
  • e17a1923fb Plots runtimes by analysis name and exechosts Mark DePristo 2011-12-07 09:24:47 -0500
  • 5d2212bc8e Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-12-07 09:03:17 -0500
  • 6bf18899df Fix for variant summary -- now treats all 50 bp deletions or insertions as CNVs Mark DePristo 2011-12-07 09:02:49 -0500
  • 5869a87e48 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-12-06 18:12:12 -0500
  • c9b2cd8ba5 Fix for chartl's stale null representation issue. Matt Hanna 2011-12-06 18:05:17 -0500
  • 79d18dc078 Fixing indexing bug on the ACsets. Added unit tests for the Exact model code. Eric Banks 2011-12-06 16:17:18 -0500
  • b4b7ae1bd9 Revved Picard to incorporate tfennell's AsyncSAMFileWriter. Removed DbSnpFileGenerator and related files as they were removed from PPP r2063 by ktibbett. Khalid Shakir 2011-12-06 10:32:19 -0500
  • f5b977fc88 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-12-06 10:11:35 -0500
  • 4001c22a11 Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup. Matt Hanna 2011-12-06 10:10:38 -0500
  • 677bea0abd Right aligning GATKReport numeric columns and updated MD5s in tests. PreQC parses file with spaces in sample names by using tabs only. PostQC allows passing the file names for the evals so that flanks can be evaled. BaseTest's network temp dir now adds the user name to the path so files aren't created in the root. HybridSelectionPipeline: - Updated to latest versions of reference data. - Refactored Picard parsing code replacing YAML. Khalid Shakir 2011-12-05 23:04:33 -0500
  • 7a0f6feda4 Make sure that too many alternate alleles aren't being passed to the genotyper (10 for now) and exit with a UserError if there are. Eric Banks 2011-12-05 16:18:52 -0500
  • 7fac4afab3 Fixed priors (now initialized upon engine startup in a multi-dimensional array) and cell coefficients (properly handles the generalized closed form representation for multiple alleles). Eric Banks 2011-12-05 15:57:25 -0500
  • 1ba03a5e72 Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction David Roazen 2011-12-05 14:06:00 -0500
  • a7cb941417 The posteriors vector is now 2 dimensional so that it supports multiple alleles (although the UG is still hard-coded to use only array[0] for now); the exact model now collapses probabilities for all conformations over a given AC into the posteriors array (in the appropriate dimension). Fixed a bug where the priors and posteriors were being passed in swapped. Eric Banks 2011-12-04 13:02:53 -0500
  • eab2b76c9b Added loads of comments for future reference Eric Banks 2011-12-03 23:54:42 -0500
  • 29662be3d7 Fixed bug where k=2N case wasn't properly being computed. Added optimization for BB genotype case not in old model. At this point, integration tests pass except for 1 case where QUALs differ by 0.01 (this is okay because I occasionally need to compute extra cells in the matrix which affects the approximations) and 2 cases where multi-allelic indels are being genotyped (some work still needs to be done to support them). Eric Banks 2011-12-03 23:12:04 -0500
  • 71f793b71b First partially working version of the multi-allelic version of the Exact AF calculation Eric Banks 2011-12-02 14:13:14 -0500
  • d014c7faf9 Queue now properly escapes all shell arguments in generated shell scripts David Roazen 2011-11-28 13:35:14 -0500
  • b5b5ffe71d Parameterize intervals. Matt Hanna 2011-12-01 13:18:18 -0500
  • ef81224dcf Parameter to customize # CPU threads. Matt Hanna 2011-11-30 23:47:46 -0500
  • c9eae32f6e Revving Tribble to actually close file handles when close() is called. Matt Hanna 2011-11-30 22:42:21 -0500
  • 3060a4a15e Support for list of known CNVs in VariantEval Mark DePristo 2011-11-30 17:05:16 -0500
  • b65db6a854 First draft of a test script for I/O performance with the new asynchronous I/O processing. Also includes convenience parameters for specifying the IO/CPU threading balance outside of a tag. Will be killed when Queue gets better support for tagged arguments (hopefully soon). Matt Hanna 2011-11-30 13:13:16 -0500
  • 1d5d200790 Cleaned up unused import statements Laurent Francioli 2011-11-30 15:30:30 +0100
  • 28b286ad39 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-30 09:11:53 -0500
  • 20bffe0430 Adapted for the new version of MendelianViolation Laurent Francioli 2011-11-30 14:46:38 +0100
  • 1cb5e9e149 Removed outdated (and unused) -familyStr commandline argument Laurent Francioli 2011-11-30 14:45:04 +0100
  • 9574be0394 Updated MendelianViolationEvaluator integration test Laurent Francioli 2011-11-30 14:44:15 +0100
  • f49dc5c067 Added functionality to get all children that have both parents (useful when trios are needed) Laurent Francioli 2011-11-30 14:43:37 +0100
  • a4606f9cfe Merge branch 'MendelianViolation' Laurent Francioli 2011-11-30 11:13:15 +0100
  • b279ae4ead Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Laurent Francioli 2011-11-30 10:10:21 +0100
  • 7d58db626e Added MendelianViolationEvaluator integration test Laurent Francioli 2011-11-30 10:09:20 +0100
  • 91413cf0d9 Merged bug fix from Stable into Unstable Ryan Poplin 2011-11-29 14:01:23 -0500
  • cb284eebde Further updating VQSR tutorial wiki docs to reflect the bundle Ryan Poplin 2011-11-29 14:00:57 -0500
  • dcb889665d Merged bug fix from Stable into Unstable Ryan Poplin 2011-11-29 09:58:49 -0500
  • 447e9bff9e Updating VQSR tutorial wiki docs to reflect the bundle Ryan Poplin 2011-11-29 09:57:45 -0500
  • 110298322c Adding Transmission Disequilibrium Test annotation to VariantAnnotator and integration test to test it. Ryan Poplin 2011-11-29 09:29:18 -0500
  • ab67011791 Corrected bug introduced in the last update and causing no families to be returned by getFamilies in case the samples were not specified Laurent Francioli 2011-11-29 11:18:15 +0100
  • d7d8b8e380 Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now. Eric Banks 2011-11-28 14:18:28 -0500
  • a09c01fcec Removed walker argument FamilyStructure as this is now supported by the engine (ped file) Laurent Francioli 2011-11-28 17:18:11 +0100
  • 795c99d693 Adapted MendelianViolation to the new ped family representation. Adapted all classes using MendelianViolation too. MendelianViolationEvaluator was added a number of useful metrics on allele transmission and MVs Laurent Francioli 2011-11-28 17:13:14 +0100