2636d216de
Adding indel vqsr integration test
2011-09-08 10:38:13 -04:00
9cba1019c8
Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap
2011-09-08 09:25:13 -04:00
e0020b2b29
Fixing PrintRODs. Now has input and only prints out one copy of each record
2011-09-08 08:58:37 -04:00
2ded027762
Removed dysfunctional tranches support from VariantEval
2011-09-07 16:09:24 -04:00
aa9e32f2f1
Reverting Mark's previous commit as per the open discussion. Now the eval modules check isPolymorphic() before accruing stats when appropriate. Fixed the IndelLengthHistogram module not to error out if the indel isn't simple (that would have been bad). Only integration test that needed to be updated was the tranches one based on a separate commit from Mark.
2011-09-07 15:48:06 -04:00
9127849f5d
BugFix for unit test
2011-09-07 14:54:10 -04:00
da9c8ab386
Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.
2011-09-06 20:39:42 -04:00
1aa4b12ff0
Reduced the number of combinations being tested here, which was overkill
2011-09-01 10:42:43 -04:00
3af001fff2
Bugfix for file that must not exist on disk
2011-08-29 17:00:10 -04:00
1ceb020fae
UnitTests for RScript
2011-08-27 10:50:05 -04:00
c0503283df
Spelling fix requires md5 updates
2011-08-26 07:40:44 -04:00
e618cb1e79
a) Renamed/expanded SelectVariants arguments that choose particular kinds of variants and particular allelic types, now instead of -Indels or -SNPs we can specify for example -selectType [MIXED|INDEL|SNP|MNP|SYMBOLIC]. To select biallelic, multiallelic variants, use -restrictAllelesTo [BIALLELIC|MULTIALLELIC]. Corresponding gatkdocs changes.
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b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
2011-08-24 12:25:50 -04:00
1ecbf05aae
Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE
2011-08-23 23:49:36 -04:00
c4c90c8826
Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:
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- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
2011-08-22 15:13:27 -04:00
782453235a
Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants
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Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
2011-08-20 12:24:22 -04:00
4939648fd4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 08:50:43 -04:00
ff018c7964
Swapped argument order but not MD5 order
2011-08-19 16:55:56 -04:00
b08d63a6b8
Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable
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-- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments.
-- @Advanced arguments
2011-08-19 15:06:37 -04:00
269ed1206c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 09:32:20 -04:00
a5e279d697
Dynamic typing of vcf.gz files
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-- CombineVariantsIntegrationTests now use dynamic typing of vcf.gz files
-- FeatureManagerUnitTests tests for correctness.
2011-08-19 09:05:11 -04:00
58560a6d50
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 16:17:52 -04:00
3dfb60a46e
Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.
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VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
2011-08-18 16:17:38 -04:00
c2287c93d7
Cleanup of codec locations. No more dbSNPHelper
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-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper. rsID function now in VCFutils. Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move
2011-08-18 10:02:46 -04:00
b75a1807e3
Adding integration test to cover sample exclusion
2011-08-17 22:40:09 -04:00
53006da9a5
Improved descriptions for the SnpEff annotations in the VCF header
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(based on Eric's feedback).
2011-08-17 16:09:10 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
9d2cda3d41
Removed a public -> private dependency in our test suite.
2011-08-12 17:29:10 -04:00
9121b8ed65
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 12:24:19 -04:00
7ed120361d
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
2011-08-12 12:23:44 -04:00
27f0748b33
Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
2011-08-12 11:11:56 -04:00
005bd71be3
Working too quickly earlier. Fixing syntax.
2011-08-12 10:29:36 -04:00
c7ca33cbff
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 10:12:09 -04:00
639a01f382
Updating integration test now that VE has been updated
2011-08-12 07:15:08 -04:00
41f3da75d7
Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.
2011-08-12 02:22:44 -04:00
45f973ab1f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 00:40:18 -04:00
eba316621d
Finish moving VE over to new rod system and fixing up the type inconsistency between eval and comp rods. Now the novel count is always 0 under the known stratification. :)
2011-08-12 00:40:08 -04:00
9de06560df
Update to new RodBinding system
2011-08-11 17:54:16 -04:00
f1d1252be2
Fixing syntax of BQSR and UG performance tests.
2011-08-11 17:04:09 -04:00
902eb0c61e
Adding dbsnp annotation back into the UG integration tests
2011-08-11 13:55:03 -04:00
c7b9a9ef0a
Updating UnifiedGenotyper to use the new rod binding system.
2011-08-11 11:02:11 -04:00
79c86e211f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 09:59:20 -04:00
ea42ee4a95
Updating BQSR for the new rod binding system.
2011-08-11 09:58:42 -04:00
8cdc0cbd9c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 08:58:49 -04:00
40e06f9afb
Fixed broken RodBinding defaults.
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-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
2011-08-11 08:58:30 -04:00
bdb1da30fd
Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.
2011-08-10 22:43:08 -04:00
07ad8c78a9
More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.
2011-08-10 14:24:40 -04:00
8d14d32a62
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-10 13:42:37 -04:00
749c8bfbcd
Moving more tools over to the new rod system
2011-08-10 13:42:35 -04:00
0497170bc9
SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.
2011-08-10 13:12:09 -04:00
a42f90db11
Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.
2011-08-10 12:20:18 -04:00
Ryan Poplin
Mark DePristo
Eric Banks
Guillermo del Angel
Khalid Shakir
David Roazen
Menachem Fromer