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
c60cf52f73
Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.
2011-08-10 10:20:37 -04:00
1ea5ec276b
Minor cleanup
2011-08-09 23:28:59 -04:00
bc2d4f554d
Bringing Indel Realigner up to speed with the new rod binding syntax; now use -known to specify the known indels track.
2011-08-09 23:21:17 -04:00
489e5cffc1
Missed a few 'variants'
2011-08-09 14:29:15 -04:00
b20c4d5286
Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.
2011-08-09 12:04:55 -04:00
7afb5c9f1c
More updates to be consistent with the new rod syntax.
2011-08-09 10:11:37 -04:00
1e490e0dec
Bringing up to speed with new syntax
2011-08-09 09:26:06 -04:00
70b3daf689
VariantsToVCF is up and running again; integration tests are reenabled (and added one for dbSNP).ant
2011-08-09 03:03:43 -04:00
2efa376619
Made the necessary changes to get SnpEff support working with the new rodbinding system.
2011-08-08 23:29:39 -04:00
b180a1311a
Merge branch 'snpEff'
2011-08-08 22:12:14 -04:00
28d8c8fcbc
Modified the SnpEff integration test to run on a much smaller interval.
2011-08-08 21:51:16 -04:00
a13bc7b929
Added an integration test for the SnpEff annotation support, as well as some extra safety checks and comments.
2011-08-08 20:01:24 -04:00
80924d24de
Single positional arguments are now treated as names unless they actually match a tribble feature
2011-08-08 19:26:27 -04:00
f8a56bc64b
Merge branch 'master' into rodRefactor
2011-08-08 16:58:18 -04:00
f8ad91b16f
Reverting a bunch of bad -B type drops
2011-08-08 16:57:38 -04:00
5e288136e0
Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself.
2011-08-08 16:51:43 -04:00
d7813db217
Combine Variants was actually outputting invalid VCFs in cases where it was combining Variant Contexts with different alternate alleles: if any of the genotypes had PLs they were no longer valid/correct. Added a check for such cases (the combined VC has more alleles than an original VC) and strip out the PLs when triggered; added integration test to cover it. I also added the check to Select Variants, although it currently doesn't remove unused alleles so it should never trigger. Is there any reason not to strip out unused alleles after a select?
2011-08-08 16:25:35 -04:00
4f8fc0f2f1
VCF3 now dynamically determined
2011-08-08 15:05:47 -04:00
ba7353c561
Updated IntegrationTests to use the new type free format for VCF files
2011-08-08 15:04:38 -04:00
0810c42309
GATK now does dynamic type determination for VCF files
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Added UnitTests covering all of the cases.
2011-08-08 14:45:46 -04:00
e36994e36b
Refactored a FeatureManager class from RMDTrackBuilder
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New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK.
Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.
2011-08-08 14:04:46 -04:00
e5fde0d16b
Merge branch 'master' into rodRefactor
2011-08-08 10:08:43 -04:00
526b524c3c
CombineVariants with new RodBinding. Bugfix
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-- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run
-- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.
2011-08-07 20:16:51 -04:00
6693407bd8
Merged bug fix from Stable into Unstable
2011-08-07 17:39:03 -04:00
1d8b1bae0a
Need to rename the integration test argument -mask to -maskName
2011-08-07 13:32:26 -04:00
ece8f0db5e
Added b37dbSNP129, needed for Queue
2011-08-07 11:26:07 -04:00
b0e91f85cf
fix merge from Khalid's Queue fix
2011-08-07 10:33:20 -04:00
4d88e72958
Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/test/org/broadinstitute/sting/BaseTest.java
2011-08-07 10:32:27 -04:00
f049461120
Changed @Argument to @Input on input RodBindings.
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Changed shortname collision with longname.
Restored scala builds.
Updated HSP to use new syntax.
2011-08-06 20:44:19 -04:00
573700d18d
Adding missing import
2011-08-04 21:57:00 -04:00
14e43c3382
Final fix to RodBindingUnitTest to reset global counter variable
2011-08-04 21:52:39 -04:00
9308fbe3fb
VariantEval Integration Test parameterized for new novelty stratification
2011-08-04 18:08:47 -04:00
98a96f07c1
Updated standard deviation parameter in VQSR to our current recommended value
2011-08-04 14:06:26 -04:00
58a60d4901
Merge branch 'master' into rodRefactor
2011-08-04 12:48:56 -04:00
d2078f09b2
Minor fixes to ITs
2011-08-04 12:47:55 -04:00
f10588420c
Fixing path to dbSNP file as the other one was replaced
2011-08-04 12:36:24 -04:00
f0d798d47c
Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.
2011-08-04 12:06:10 -04:00
490ca475fc
Replacing hardcoded dbsnp129 with BaseTest variable
2011-08-03 22:15:22 -04:00
a831af1166
Another misprint when removing the references to -D
2011-08-03 21:29:21 -04:00
d0279bb28c
RodBinding names are now defaulting to the ArgumentTypeDescriptor fullname
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Nearly all of the tools are passing integrationtests
2011-08-03 20:48:11 -04:00
d8f1ebf8c6
Parameterized RecalibrationWalkers with clean unstable database
2011-08-03 20:06:00 -04:00
41b3840d26
Took latest VEIT and updated to use dbsnp132 vcf
2011-08-03 18:40:32 -04:00
0ef85647f7
A working version of a GATKReportDiffableReader for the diffEngine!
2011-08-03 18:21:18 -04:00
acbd3d0922
Fixing up integration tests so more
2011-08-03 17:26:35 -04:00
8f696c7731
Continuing progress towards RodBinding 1.0
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-- Cleaning up old interface to RMDT, docs and contracts added
-- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type
2011-08-03 17:19:28 -04:00
800bb97f0b
Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser
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Updated all walkers that used the now deleted methods.
2011-08-03 16:04:51 -04:00
79e4a8f6d3
Merge
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-03 15:09:47 -04:00
b25140db83
Contracts and documentation for some of RefMetaDataTracker
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Continuing to fix integration tests that don't pass / run
2011-08-03 13:34:20 -04:00
3de10b1ef8
Fixing misprint from Ryan's commit
2011-08-03 12:37:50 -04:00
db2e0aaa1a
Darn, forgot to update unit tests.
2011-08-03 12:31:08 -04:00
020b2408a8
Adding integration test for left alignment of indels
2011-08-03 12:19:44 -04:00
5dc324ff35
Dealing with merge confict
2011-08-03 11:03:47 -04:00
7c89fe01b3
Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.
2011-08-03 11:00:36 -04:00
d9bc673ff2
Fixed bad constructor in RMDTUnitTest
2011-08-03 09:42:43 -04:00
5dcac7b064
GATKReport v0.2:
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- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
2011-08-03 00:24:47 -04:00
2874835997
Bug fix for type checking RodBindings
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Now compares the feature class not the codec class.
UnitTests improvements
integrationtests on their way to actually running
2011-08-02 22:25:41 -04:00
b5e843f8f0
Approaching the end for the new RodBinding system
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-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
2011-08-02 22:00:06 -04:00
83891271b5
--variants throughout integrationtests
2011-08-02 20:28:47 -04:00
3a27a25cfc
Validates that the tribble binding provides the right object types at startup
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Tests to ensure this remains working
2011-08-02 20:11:24 -04:00
b2cde87378
Removing --DBSNP syntax from BQSR integration tests
2011-08-02 15:34:38 -04:00
e4a67f3df1
RefMetaDataTracker has complete set of get() functions for List<RodBinding<T>>
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Including unit tests
2011-08-02 14:28:35 -04:00
03741fb640
Merge branch 'master' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-02 14:21:58 -04:00
a366f9a18d
Updating tools to use the RodBinding<T> syntax
2011-08-02 14:05:51 -04:00
b9d0d2af22
Adding back temporarily removed integration test now that the file permissions have been fixed.
2011-08-02 12:39:11 -04:00
1c387848de
No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.
2011-08-02 10:39:50 -04:00
2c5e526eb7
Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.
2011-08-02 10:34:46 -04:00
5626199bb6
The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
2011-08-02 10:14:21 -04:00
8b1adb8c95
Removed getVariantContext() code
2011-08-01 13:41:09 -04:00
Guillermo del Angel
Mark DePristo
Eric Banks
David Roazen
Menachem Fromer
Ryan Poplin
Khalid Shakir