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  • 9be4f6894c Adding GGA integration test to HaplotypeCaller. Ryan Poplin 2012-05-30 15:21:18 -0400
  • 5dd811f84a Adding genotype given alleles mode to the HaplotypeCaller. Ryan Poplin 2012-05-30 15:07:01 -0400
  • d09b8d5584 Fixing docs Eric Banks 2012-05-30 13:24:08 -0400
  • d6e1205310 Updating default values for DiagnoseTargets Mauricio Carneiro 2012-05-30 10:48:45 -0400
  • f987d5487e Adding RMSE value to the plots produced by CalibrateGenotypeLikelihoods. Ryan Poplin 2012-05-30 11:27:53 -0400
  • 12da794116 Smooth geom plotted on the main CalibrateGenotypeLikelihood plots wasn't using the weight of the data points for fitting. Ryan Poplin 2012-05-30 09:44:39 -0400
  • 1fa88fd389 Fixing some problems with the binary release tests David Roazen 2012-05-29 16:11:17 -0400
  • 2908fb77e0 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-05-29 15:52:57 -0400
  • ebc3ff680f Bug fix for CalibrateGenotypeLikelihoods. There is no overall read group when in external likelihoods mode. Added integration test for external likelihoods mode. Ryan Poplin 2012-05-29 15:50:00 -0400
  • 5e76c811b9 Build system round 2: finished preparing the packaging system for dual protected/lite releases David Roazen 2012-05-24 12:05:14 -0400
  • c3c7f17d90 Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. Instead of creating a supposed network temporary directory locally which then fails when remote nodes try to access the non-existant dir, now checking to see if they network directory is available and throwing a SkipException to bypass the test when it cannot be run. TODO: Throw similar SkipExceptions when fastas are not available. Right now instead of skipping the test or failing fast the REQUIRE_NETWORK_CONNECTION=false means that the errors popup later when the networked fastas aren't found. Khalid Shakir 2012-05-29 11:18:22 -0400
  • b8b139841d DiagnoseTargets with working Q1,Median,Q3 Roger Zurawicki 2012-04-12 18:54:29 -0400
  • 50031b63c5 Fix possible NPE from NBaseCount annotation module Eric Banks 2012-05-29 09:46:00 -0400
  • 08de4dfd96 Missed one integration test Mark DePristo 2012-05-29 07:23:24 -0400
  • 454c8e63e6 Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s Mark DePristo 2012-05-28 20:20:05 -0400
  • 7ce24a96f1 PBT now uses getGenotypeLikelihoodString to avoid NPE when there are no PLs present Mark DePristo 2012-05-28 20:18:16 -0400
  • 1818c29371 Fixed long-standing bug in beagle codec that was passing on the header record for decoding Mark DePristo 2012-05-28 20:17:26 -0400
  • dcad4b865c build.xml now copies report files to ~/private_html for convenient viewing Mark DePristo 2012-05-28 10:22:09 -0400
  • 06b02e1b9b Update MD5s to reflect new limited output of DiffObjectsWalkers Mark DePristo 2012-05-27 11:20:47 -0400
  • 5894d045cb Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests Mark DePristo 2012-05-27 11:13:43 -0400
  • 86e5a066fc Even more conservative limit on number of differences to summarize at 1000 Mark DePristo 2012-05-26 14:44:37 -0400
  • 31f4e5b52e Stop unlimited runtimes in DiffEngine when you have lots of differences Mark DePristo 2012-05-26 09:05:54 -0400
  • a6ee4f98b5 Yet More missing md5's Guillermo del Angel 2012-05-25 17:21:47 -0400
  • 4efa3040ce More missing md5's Guillermo del Angel 2012-05-25 17:20:04 -0400
  • 4109fcbb08 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-05-25 13:03:05 -0400
  • 2be5704a25 Fixed haplotype boundary bug in PairHMMIndelErrorModel Mauricio Carneiro 2012-05-25 12:16:28 -0400
  • 175bb35e70 Made TandemRepeatAnnotator standard annotation. HRun no longer standard (superceded by former) Guillermo del Angel 2012-05-25 12:56:23 -0400
  • d6df817174 Oops, don't enable shadow BCF tests Mark DePristo 2012-05-24 13:31:13 -0400
  • 0a86564669 Updated test files didn't make it into last push Mark DePristo 2012-05-24 13:29:44 -0400
  • 7280cdf937 Bugfixes and testdata cleanup Mark DePristo 2012-05-24 13:26:05 -0400
  • 57a1ac0888 Fix up bad paths to public/testdata files Mark DePristo 2012-05-24 10:54:27 -0400
  • e9c22b9aad Final updates to integration tests for BCF2 Mark DePristo 2012-05-24 10:50:33 -0400
  • ade1843818 Bugfix for not setting header in AbstractVCFCodec Mark DePristo 2012-05-22 16:40:01 -0400
  • 6ca71fe3b4 GATK tests use public/testdata not /humgen/ as much as possible Mark DePristo 2012-05-22 16:27:13 -0400
  • cad608c07f Adding as many test data files into public/testdata as possible Mark DePristo 2012-05-22 16:26:28 -0400
  • 69ee4d0454 Moved getMetaDataForField to VariantContextUtils Mark DePristo 2012-05-22 07:14:46 -0400
  • cb13f16e90 WalkerTest infrastructure to generate and test shadowBCF file for every generated VCF file Mark DePristo 2012-05-21 16:38:58 -0400
  • f77d2e6965 Renamed NO_HEADER to the more accurate no_cmdline_in_header Mark DePristo 2012-05-21 16:38:28 -0400
  • 4bde24f020 Bugfix for VCFWriter in the case where there are no genotypes in the VC but genotypes in the header Mark DePristo 2012-05-21 16:24:23 -0400
  • 4846bf5c8e @Hidden --also_generate_bcf engine argument produces both VCF and BCF files for -o my.vcf Mark DePristo 2012-05-21 11:19:57 -0400
  • bb0d87666a Finally just deleted equals() method in GATKArgumentCollection. Mark DePristo 2012-05-21 10:59:31 -0400
  • 6f469305ab Don't try to share BCF2 yet Mark DePristo 2012-05-21 10:50:59 -0400
  • c8ed0bfc4c Edge case fixes for BCF2 Mark DePristo 2012-05-18 15:49:23 -0400
  • 40431890be -- BCF2 is now a reference dependent codec so it can initialize the contigs in the case where the file doesn't have contigs in it -- BCF2 writer can now work without the contig lines being in the header -- Made GenomeLocParser a final class Mark DePristo 2012-05-18 11:38:51 -0400
  • 6301572009 GenotypeLikelihood PLs are capped at Short.MAX_INT now Mark DePristo 2012-05-18 09:04:59 -0400
  • d52bc31a47 Bugfix for doNotWriteGenotypes mode Mark DePristo 2012-05-17 13:20:16 -0400
  • 64d4238e2f 99% working version of BCF2 encoder / decoder Mark DePristo 2012-05-17 09:54:50 -0400
  • b5bce8d3f9 AD should be UNBOUNDED, actually Mark DePristo 2012-05-16 20:33:46 -0400
  • ac7460ef8c New complex VCF files for testing Mark DePristo 2012-05-16 20:22:26 -0400
  • aaf11f00e3 Near final BCF2 implementation Mark DePristo 2012-05-16 20:21:03 -0400
  • dfee17a672 Generalize / unify code for handling strings Mark DePristo 2012-05-16 08:59:26 -0400
  • b4a5acd6f4 Added some genotype tests for BCF2, which all pass. Of course that's because I commented out the ones that didn't Mark DePristo 2012-05-15 16:34:29 -0400
  • 373ae39e86 Testing of BCF codec Mark DePristo 2012-05-15 14:39:12 -0400
  • fb1911a1b6 -- Convenience constructor for VariantContextBuilder that creates a new one based on an existing builder -- Convenience routine for creating alleles from strings of bases -- Convenience constructor for VCFFilterHeader line whose description is the same as name -- VariantContextTestProvider creates all sorts of types of VariantContexts for testing purposes. Can be reused throughtout code for BCF, VCF, etc. -- Created basic BCF2WriterCodec tests that consumes VariantContextTestProvider contexts, writes them to disk with BCF2 writer, and checks that they come back equals to the original VariantContexts. Actually worked for some complex tests in the first go Mark DePristo 2012-05-14 19:57:39 -0400
  • 4968dcd36a Throw an error when genotype fields with mixed vector lengths are encountered Mark DePristo 2012-05-14 15:38:50 -0400
  • afd2f1a3f9 Individual VariantContextWriters are now package protected Mark DePristo 2012-05-14 15:34:32 -0400
  • 24864fd5b0 GATK now writes BCF output to any file with .bcf extension Mark DePristo 2012-05-14 15:19:39 -0400
  • e2311294c0 Removed unused ManualSortingVCFWriter Mark DePristo 2012-05-14 09:46:06 -0400
  • 93cef82637 BCF2 header encoding decoding at final spec Mark DePristo 2012-05-12 19:59:00 -0400
  • ce9e9eebb1 No dictionary in header. Now built dynamically from the header in the writer and codec Mark DePristo 2012-05-12 13:07:08 -0400
  • f0b081a85f Update VCF.jar loading test Mark DePristo 2012-05-12 12:50:55 -0400
  • c3b8048e2e Moving around classes in VCF and BCF2 Mark DePristo 2012-05-12 12:24:56 -0400
  • 679ffdd333 Move BCF2 from private utils to public codecs Mark DePristo 2012-05-12 12:13:33 -0400
  • d13cda6b6f Update encoding / decoding of genotypes to final spec version Mark DePristo 2012-05-12 12:09:29 -0400
  • 0921c3096c -- Disable genotype filtering since it doesn't work -- Update code to name new, more general decodeSingleValue -- Update MISSING_VALUE constants to be 0xFFFFFF80 vs. 0x00000080 as these are equivalent for a byte and handle the two complement cast from byte to int -- Fix decoding of byte and short values which were screwing up missing values -- Code cleanup in decoder -- Generalize bestIntegerType function -- Handle the encoding of boolean FLAG fields -- Test the encoding of vectors of values Mark DePristo 2012-05-12 11:45:56 -0400
  • c0c4599fe1 Cleanup naming of encoder functions for clarity Mark DePristo 2012-05-11 12:34:40 -0400
  • 1d39a9227b Low-level encoder / decoder unit tests and code cleanup Mark DePristo 2012-05-11 11:27:46 -0400
  • 443c83d4a7 Removed old STRING_BY_REF types Mark DePristo 2012-05-10 22:13:46 -0400
  • 450f098a61 BCF2 encoder / decoder implement new site / genotype block organization Mark DePristo 2012-05-10 17:43:18 -0400
  • 27b51d4dea Enable on the fly indexing of BCF2 Mark DePristo 2012-05-10 12:56:22 -0400
  • 81ab0dd051 Implement separate data blocks for sites and genotypes data Mark DePristo 2012-05-10 12:28:25 -0400
  • fd988274c1 Separate the BCF2 codec from the BCF2 decoder Mark DePristo 2012-05-10 12:17:38 -0400
  • 81bd7646d6 Fix for MISSING floats Mark DePristo 2012-05-10 11:29:57 -0400
  • 931b575748 More BCF2 improvements Mark DePristo 2012-05-09 18:51:02 -0400
  • 3afbc50511 More BCF2 improvements Mark DePristo 2012-05-09 17:55:42 -0400
  • 7541b523e1 BCF improvements Mark DePristo 2012-05-09 13:47:56 -0400
  • 0799855479 Archiving GCF Mark DePristo 2012-05-09 10:43:30 -0400
  • 085588cb04 Not Nexus. Need new name. Navel? Joel Thibault 2012-05-24 10:07:59 -0400
  • 43919078cd Merged bug fix from Stable into Unstable Guillermo del Angel 2012-05-23 21:21:01 -0400
  • 4bc04e2a9e Correct way in which start/stop positions in a VC are computed when creating an indel VC. Old way was incorrect in case GENOTYPE_GIVEN_ALLELES was specified with a complex record. New way should work in general for all cases and is simpler. Guillermo del Angel 2012-05-23 21:19:30 -0400
  • 7fe07a4ae6 Bug fix: prevent index out of bounds error if reference sample in pool caller has a call present at a site but genotype is a no-call allele Guillermo del Angel 2012-05-22 21:06:53 -0400
  • dad75babf1 Increase Queue memory limits to 16 GB Joel Thibault 2012-05-22 10:30:08 -0400
  • af3d73b884 Re-enable partitioning for Mongo reads (but not writes) Joel Thibault 2012-05-21 17:04:16 -0400
  • 692addb498 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-05-22 10:25:03 -0400
  • c3fb321014 Minor updates to pacbio data processing script to make it work with the latest bwa version/settings. Ryan Poplin 2012-05-22 10:24:45 -0400
  • d366cce714 Initial commit of a burden testing framework. Currently tests against only one phenotype and only one weighting function, but computes robust weighted dosages and calls into an R script that calculates both a direct glm LRT and an asymptotic normal p-values. Weights currently read in from external file (beta-values). Future work is to let these be calculated on the fly from e.g. annotation, potential impact, conservation, etc, and enable multiple weighting schemes tested jointly for association against multiple phenotypes. Christopher Hartl 2012-05-21 16:56:32 -0400
  • 08dfd6cab6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-05-21 16:47:07 -0400
  • 04000d920c Bug fix in BadCigar read filter for index out of bounds exception when used with a bam file that contains unmapped reads. Ryan Poplin 2012-05-21 16:46:59 -0400
  • 94cd4e6a7d Updated WGP min confidence from 4 to 10 based on recommendations from depristo and ebanks. Khalid Shakir 2012-05-21 16:41:21 -0400
  • 666862af19 Added @Hidden option for GSA production use to cap the max alleles for indels at a lower number than for SNPs Eric Banks 2012-05-21 16:03:29 -0400
  • e57cd78bba Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each. This bug will happen in all adapter/wrapper classes that are passed a resource, and then in their close method they ignore requests to close the wrapped resource, causing a leak when the adapter is the only one left with a reference to the resource. Khalid Shakir 2012-05-21 15:41:27 -0400
  • 7f5ec17d22 Fixed up the comments in the GATKReportTable code and added some sanity checks to make sure that the user doesn't inconsistently add rows and corresponding IDs to the table. Eric Banks 2012-05-21 14:16:13 -0400
  • 27c46b8071 Better matching and searching between sites and samples Joel Thibault 2012-05-15 16:12:39 -0400
  • 8fb6fc9ff9 Contigs as blocks are too large for MongoDB documents Joel Thibault 2012-05-15 14:47:42 -0400
  • c1c70f3b41 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-05-21 09:39:08 -0400
  • 92d8aa3d4c Don't exception out in these VE modules if the VCF has records that aren't just SNPs or indels Eric Banks 2012-05-21 09:38:52 -0400
  • 5cc9a12fbb Fixed definition in VCF header for pool caller genotype parameters MLAC and MLAF Guillermo del Angel 2012-05-19 14:53:37 -0400
  • 3af3834d50 Fixing 2 bugs in the SAMRecord printing argument descriptor code (as reported by Kristian): Eric Banks 2012-05-18 11:55:41 -0400
  • 26968ae8eb Forgot that the VCFStreamingOntegrationTest uses VE Eric Banks 2012-05-18 02:51:53 -0400
  • 52c206d5db Has anyone else ever noticed that the DiffEngine outputs were always doubled for some reason? That no longer happens with the new reports. Eric Banks 2012-05-18 02:32:20 -0400