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
d7f98e5c2a
Fixed merge conflict deleting a {
2011-08-04 18:48:34 -04:00
75632abf88
Merge branch 'master' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
2011-08-04 18:44:14 -04:00
f21f7f6335
SelectVariants fully documented, now the shining example of the new RodBinding system.
2011-08-04 18:28:59 -04:00
9308fbe3fb
VariantEval Integration Test parameterized for new novelty stratification
2011-08-04 18:08:47 -04:00
9be1ee59cc
TODO comments for Eric
2011-08-04 18:07:50 -04:00
a8eb8c27f0
a) Minor changes to indel consensus scripts to better reflect good default values, b) Fixed up Mills/Devine codec so it always produces correct ref padded bases, and added option to VariantsToVCF to fix reference base
2011-08-04 15:34:49 -04:00
58a60d4901
Merge branch 'master' into rodRefactor
2011-08-04 12:48:56 -04:00
e48492f3c3
Validate that the reference padding base for indels is correct.
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
f6563c0f9f
Removed support for RMD in @Requires and @Allows
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Merge as well
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 15:36:55 -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
38efd3066c
Bug fix for mask RodBinding
2011-08-03 14:58:18 -04:00
f62f47d476
Not sure why this didn't fail before, but bringing VE up to date with previous changes
2011-08-03 14:27:07 -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
f6648e0144
Don't left-align complex indels because it's too complicated.
2011-08-03 12:03:50 -04:00
85c67e9891
Contracts and documentation for Rodbinding
2011-08-03 11:16:06 -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
d3437e62da
Added a simple utility method Utils.optimumHashSize() to calculate the optimum
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initial size for a Java hash table (HashMap, HashSet, etc.) given an expected
maximum number of elements. The optimum size is the smallest size that's
guaranteed not to result in any rehash / table-resize operations.
Example Usage:
Map<String, Object> hash = new HashMap<String, Object>(Utils.optimumHashSize(expectedMaxElements));
I think we're paying way too heavy a price in unnecessary rehash operations across
the GATK. If you don't specify an initial size, you get a table of size 16 that gets
completely rehashed and doubles in size every time it becomes 75% full. This means you
do at least twice as much work as you need to in order to populate your table:
(n + n/2 + n/4 + ... 16 ~= (1 + 1/2 + 1/4...) * n ~= 2 * n
2011-08-02 21:59:06 -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
df37716857
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 18:27:13 -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
c0653514b3
minor update to comment in UG
2011-08-02 13:34:48 -04:00
Mark DePristo
Khalid Shakir
Guillermo del Angel
Eric Banks
David Roazen
Ryan Poplin