f29cadd7e2By default, don't quantize quals in BQSRv2
Eric Banks
2012-07-14 23:49:48 -0400
75543a3f22ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.
Eric Banks
2012-07-13 18:50:27 -0400
44c532531bVC priority list needs to be updated after removing unassembled haplotypes.
Ryan Poplin
2012-07-13 16:50:08 -0400
443f02ffc2Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-07-13 16:09:24 -0400
c978e37e5cupdating HC integration tests for all these changes
Ryan Poplin
2012-07-13 16:09:11 -0400
6dfcc486e8In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
Khalid Shakir
2012-07-13 15:40:56 -0400
5d0a7335earemove unnecessary use in the PRIORITY list remove unneeded imports
Ami Levy Moonshine
2012-07-13 15:19:45 -0400
d553905d79Don't try to genotype both an unassembled symbolic allele and a fully assembled insertion if they both start at the same location. Bug fix for the case of multiple indels that when all combined together make an MNP.
Ryan Poplin
2012-07-13 15:22:22 -0400
fd3bf36ed9changed license
Ami Levy Moonshine
2012-07-13 14:23:50 -0400
3ab5e2c64bDon't try to combine together unassembled, symbolic alleles.
Ryan Poplin
2012-07-12 21:20:14 -0400
d70bb59182HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.
Ryan Poplin
2012-07-10 14:22:23 -0600
75e5a50b8aMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-07-10 12:53:00 -0600
279dff9f81Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants
Guillermo del Angel
2012-07-10 13:59:00 -0400
d7bf74fb7eUpdating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.
Eric Banks
2012-07-10 02:04:26 -0400
83e33d14c5Bug fix in the merging of events into complex substitutions.
Ryan Poplin
2012-07-05 16:00:18 -0400
c2e1dc63ffMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-07-05 10:37:40 -0400
729c5e878dBug fix in the merging of events into complex substitutions.
Ryan Poplin
2012-07-05 10:37:04 -0400
dd571d9aa0Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.
Eric Banks
2012-07-04 01:22:20 -0400
33306d2e20Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.
Eric Banks
2012-07-04 00:21:21 -0400
7d30558e6fOnly 'pad' the cycle covariate for indels, not substitutions
Eric Banks
2012-07-03 23:47:01 -0400
f09141bd2fAdd a Mongo tester which outputs BCFs
Joel Thibault
2012-07-03 14:45:32 -0400
22f1afddaaMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-07-03 14:55:59 -0400
617eebd204More misc cleanup
Eric Banks
2012-07-03 14:55:37 -0400
344c3aeb1dCleanup from previous commit
Eric Banks
2012-07-03 14:42:44 -0400
9e8e78de15Adding the model name to the VQSR filter lines so that they don't get clobbered with consecutive VQSR runs for SNPs and then indels.
Ryan Poplin
2012-07-03 14:30:37 -0400
0b37d44b0dOptimizations for the RecalDatum to make BQSR (Count Covariates) much faster. Needs some cleanup.
Eric Banks
2012-07-03 13:05:11 -0400
031322ff00Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-07-03 00:12:59 -0400
a4670113bdRefactored/renamed the nested integer array; cleaned up code a bit.
Eric Banks
2012-07-03 00:12:33 -0400
f92139dd82Ooops, UG VA path for rank sum tests aren't happy with empty lists. Disabling clipping rank sum test for now.
Ryan Poplin
2012-07-02 21:12:42 -0400
7aa3f04402Updating HC integration tests.
Ryan Poplin
2012-07-02 20:43:52 -0400
7e7b4cd1b9Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-07-02 16:37:54 -0400
b807ff63efHaplotypeCaller now creates MNP and complex substitutions by using LD information to decide if events segregate together on haplotypes. Added unit test.
Ryan Poplin
2012-07-02 16:37:39 -0400
3cea080aa8Cache SoftStart() and SoftEnd() in the GATKSAMRecord
Mauricio Carneiro
2012-07-02 12:29:31 -0400
88a02fa2cbFixing but for reads with cigars like 9S54H
Mauricio Carneiro
2012-07-02 12:28:28 -0400
9ee58d323aPass the original GATK unsafe parameter to the VcfGatherFunction
Joel Thibault
2012-07-02 15:37:23 -0400
1b0a775773Disabling bcf2 reading from samtools because it's 1 basis; updating select variants integrationtest
Mark DePristo
2012-07-02 15:55:42 -0400
cac72bce91Initial version of int indexed mapping for BQSR. Will be cleaned up in a bit.
Eric Banks
2012-07-02 14:33:33 -0400
602729c09dMoved parallel tests from SelectVariants to separate SelectVariantsParallelIntegrationTest
Mark DePristo
2012-07-02 11:40:28 -0400
bcd2e13d8bAdding duplicate header line keys is a logger.debug not logger.warn message now
Mark DePristo
2012-07-02 11:39:34 -0400
01e04992f8Fixed compatibilities in AbstractVCFCodec that resulted in key=; being parsed as written as key; in VCF output
Mark DePristo
2012-07-02 11:38:59 -0400
c94c8a9c09Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-07-02 08:53:01 -0400
337e434c01Test files for LENIENT_VCF_PROCESSING and repairing VCF headers
Mark DePristo
2012-07-01 15:52:04 -0400
7aff4446d4Added unit tests for header repairing capabilities in the GATK engine
Mark DePristo
2012-07-01 15:38:10 -0400
480b32e759BCF2 is now officially zero-based open-interval, and that's how the GATK does it now
Mark DePristo
2012-07-01 14:59:27 -0400
b6093ff02cMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-07-01 10:32:37 -0400
9b87dcda4fFixing remaining integration test errors. Adding missing ex2.bcf
Mark DePristo
2012-06-30 16:23:11 -0400
d7d140eb10Move archived qscripts from private/scala to private/archive/scala
David Roazen
2012-06-30 13:15:57 -0400
6dc8f7c049Revert "Moving scala archive files to the actual archive"
David Roazen
2012-06-30 13:04:40 -0400
1ff2384c0cRevert "Removing extra directory level"
David Roazen
2012-06-30 13:04:20 -0400
40c03ab2f5Removing extra directory level
Mark DePristo
2012-06-30 12:16:09 -0400
955bab0802Moving scala archive files to the actual archive
Mark DePristo
2012-06-30 11:37:27 -0400
5ad9a98a15Minor bugfixes / consistency fixes to filter strings of Genotypes and AC/AF annotations
Mark DePristo
2012-06-30 11:22:27 -0400
6ebefcc89fAdded contig and info field header lines
Mark DePristo
2012-06-29 15:01:53 -0400
385a3c630fAdded check in VariantContext.validate to ensure that getEnd() == END value when present
Mark DePristo
2012-06-29 15:01:27 -0400
893630af53Enabling symbolic alleles in BCF2
Mark DePristo
2012-06-29 13:55:52 -0400
16276f81a1BCF2 with support symbolic alleles
Mark DePristo
2012-06-28 22:36:26 -0400
86feea917eUpdating MD5s to reflect new FT fixed count of 1 not UNBOUNDED
Mark DePristo
2012-06-28 16:40:16 -0400
6bea28ae6fGenotype filters are now just Strings, not Set<String>
Mark DePristo
2012-06-28 14:27:09 -0400
f631be8d80UnifiedGenotyperEngine.calculateGenotypes() is not only used in UG but in other walkers - vc attributes shouldn't be inherited by default or it may cause undefined behaviour in those walkers, so only inherit attributes from input vc in case of UG calling this function
Guillermo del Angel
2012-06-29 23:51:52 -0400
14274c43d9Added integration tests for true pools, using a 1 MB extract from the 93-pool large scale validation data. Test -glm BOTH and -glm INDEL
Guillermo del Angel
2012-06-29 14:22:33 -0400
b945fb22a1Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-06-29 14:21:46 -0400
cbc79443b0Add intervals file option to Tester scripts
Joel Thibault
2012-06-29 12:50:28 -0400
f95b9848b4Add new scripts for VCF and BCF testing
Joel Thibault
2012-06-28 16:24:15 -0400
256704c03dCopy intervals/intersection processing to new MongoDBIntersection file
Joel Thibault
2012-06-27 14:17:25 -0400
23e13df9d4Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-06-29 11:31:08 -0400
65037b87daMerge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-06-29 11:08:44 -0400
5a9a37ba01Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)
Guillermo del Angel
2012-06-29 11:06:12 -0400
96ea334bf2Disable caching in BQSR for now since it significantly slows down computation; will look into this in a bit.
Eric Banks
2012-06-28 15:27:44 -0400
e9d750297aUpdates for the inline/extended attributes split
Joel Thibault
2012-06-28 10:03:37 -0400
abe74dc32dNavel -> GXDB
Joel Thibault
2012-06-27 14:09:30 -0400
05791ebf80Adding the Clipping rank sum test: If alternate-supporting reads have more hard clipping than reference-supporting reads this is evidence for error.
Ryan Poplin
2012-06-28 13:22:56 -0400
d12ec92a55Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-06-28 12:57:59 -0400
5bb0693888Bug fix for HC GGA mode. Shouldn't try to add an indel into the haplotype if that haplotype already contains the event of interest. Misc minor assembly param changes. Turning off capping of base qualities by base indel qualities until we can evaluate that change.
Ryan Poplin
2012-06-28 12:57:51 -0400
1ce0b9d519Throwing UnknownTribbleType exception instead of CommandLineException when an unknown tribble type is specified.
Khalid Shakir
2012-06-28 11:21:11 -0400
734bb5366bSpecial case the situation where we have ploidy == 0 (no GT values) to implicitly assume we have diploid samples
Mark DePristo
2012-06-28 10:04:15 -0400
064cc56335Update integration tests to reflect new FT header line standard and new DiagnoseTargets field names
Mark DePristo
2012-06-27 18:19:13 -0400
64d7e93209Massive bugfixes
Mark DePristo
2012-06-27 18:18:25 -0400
7144154f53VCFWriter and BCFWriter no longer allow missing samples in the VC compared to their header
Mark DePristo
2012-06-27 17:39:00 -0400
4811a00891GENOTYPE_FILTER_KEY is now a VCFStandardHeaderLine
Mark DePristo
2012-06-27 17:34:56 -0400
93426a44b1Fixes for DiagnoseTargets to be VCF/BCF2 spec complaint
Mark DePristo
2012-06-27 17:33:37 -0400
e8288c78d7A brutally complex VCF from DiagnosisTargets for testing
Mark DePristo
2012-06-27 10:58:13 -0400
dc7636b923Refactor the ContextCovariate to significantly reduce runtime
Eric Banks
2012-06-28 02:29:35 -0400
1fafd9f6c8NestedHashMap-based implementation of BQSRv2 along with a few minor optimizations. Not a huge runtime upgrade over the long bitset approach, but it allows us to implement further optimizations going forward. Integration test change because the original version had a bug in the quantized qual table creation.
Eric Banks
2012-06-27 16:55:49 -0400
21d5e8a252Small modifications to the transcript evaluator
Christopher Hartl
2012-06-27 11:29:59 -0400
a1e72ebe4eInsertSizeDistribution was totally busted, and was killing my retrogene pipeline. I'm not sure GATKReports are any longer meant to be dynamically updated, so I've altered it to calculate the histogram internally and dump it to a molten output table. Also the genotyper wants to read in a flat file, so that'll need to be changed in the near future.
Christopher Hartl
2012-06-27 11:25:21 -0400
746a5e95f3Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding. Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals. IntervalUtils return unmodifiable lists so that utilities don't mutate the collections. Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus. Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values. JobRunInfo handles the null done times when jobs crash with strange errors.
Khalid Shakir
2012-06-27 01:15:22 -0400
a5df8f1277This file shouldn't be under source control
Mark DePristo
2012-06-26 17:32:35 -0400
Eric Banks
Ryan Poplin
Khalid Shakir
Ami Levy Moonshine
Guillermo del Angel
Mauricio Carneiro
Mark DePristo
Joel Thibault
David Roazen
Christopher Hartl