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where it was combining Variant Contexts with different alternate alleles: if any of the genotypes had PLs they were no longer valid/correct.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
383bb6f0e0
Merge branch 'master' into rodRefactor
2011-08-08 15:25:55 -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
197169e47b
Submitting patch from Larry Singh to make MathUtils compatible with java 1.7
2011-08-08 13:34:04 -04:00
dd974040af
When finding the highest-impact effect at a locus, all effects that are not within a
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non-coding gene are now considered higher impact than all effects that are within a
non-coding gene.
2011-08-08 13:29:54 -04:00
c1061e994c
Initial support for adding genomic annotations through VariantAnnotator using
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the output from the SnpEff tool, which replaces the old Genomic Annotator.
2011-08-08 13:29:53 -04:00
0db79207e8
Refactored dependancy from CommandLineGATK from javadocs
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This allows us to run the GATK again in environments without Javadoc loading by default in the classpath
2011-08-08 12:27:13 -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
5f8bc3aa8a
Documenting classes, and name cleanup
2011-08-07 15:17:50 -04:00
1c63d43176
Help now points to GATKDocs instead of spitting out full, garbled description
2011-08-07 15:02:46 -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
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
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
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
2ba57bb502
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 13:30:46 -04:00
38e4ae4176
minor update to comment in UG
2011-08-02 13:30:38 -04:00
821bbfa9e0
Bug fixes and enhancements to run whole-genome indel VQSR, removed old chr20-only code and cleanup
2011-08-02 13:17:20 -04:00
65c5d55b72
Not sure how I missed these. These lines are now superfluous.
2011-08-02 12:48:36 -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
184030dd56
RefMetaDataTracker no longer automagically converts inputs to VariantContexts
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This was no longer working properly given that DBSNP indels needed to be moved around. The adaptor system is being refactored and you will need to convert files from X -> VCF for many tools to work.
2011-08-01 15:21:16 -04:00
8b1adb8c95
Removed getVariantContext() code
2011-08-01 13:41:09 -04:00
f69bff5dd6
Commented out, because these fail the now removed dbSNP conversion.
2011-08-01 13:34:25 -04:00
3a9b6eacdf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-01 11:23:18 -04:00
7b07c4e04e
RefMetaDataTracker now has get() methods accepting RodBindings
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RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
2011-07-30 15:34:11 -04:00
a6691ab2fd
List<RodBinding<T>> now working (sort of).
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At least the argument parsing system tolerates it.
2011-07-29 16:11:22 -04:00
6acb4aad3b
RodBinding<T> are properly generic now.
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VariantContextRodBinding removed, as RodBinding<VariantContext> is the right style now.
2011-07-29 14:37:12 -04:00
3b799db61a
RefMetaDataTracker cleanup and unit tests
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You know have to provide an explicit list of RODRecordLists upfront to the constructor. RefMetaDataTracker is now immutable. Changes in engine to incorporate these differences
Extensive UnitTests for RefMetaDataTracker now.
2011-07-29 13:23:17 -04:00
b06deac9ea
Merged bug fix from Stable into Unstable
2011-07-29 10:02:36 -04:00
c0d4110ffd
Correcting redundant warning text.
2011-07-29 10:01:11 -04:00
39b4e76fde
Continuing refactoring of RefMetaDataTracker.
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On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types
2011-07-28 17:48:28 -04:00
7c5c656b46
Uncovered fundamental accounting bug in VariantEval. Will be fixed by dev. team
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Problem is that Novelty sees multiple records at a site (SNP, INDEL) to calculate whether a site is novel, but VariantEvalWalker makes an arbitrary decision which to use for analysis and CompOverlap may not see a comp record of the same type as eval. So you get lines where the stratification is known but there are 10 novel sites!
2011-07-28 14:19:27 -04:00
33b32c4211
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-28 13:57:22 -04:00
7a2a65155f
Merged bug fix from Stable into Unstable
2011-07-28 13:56:43 -04:00
1afc49a297
There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.
2011-07-28 13:55:58 -04:00
f7a126722b
Cleaned up VariantContext accessors in RefMetaDataTracker
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It's no longer possible to provided allowed types, as this was a very rarely used feature in the engine. These get methods have been removed and local uses replaced with tests directly in their code. This simplified the RefMetaDataTracker significantly
VariantContextRodBinding now forwards along all of the RefMetaDataTracker methods, so it is possible to create a full equivalent VariantContextRodBinding now as a walker field variable.
All walkers updated to the new RefMetaDataTracker function call style
2011-07-28 00:16:34 -04:00
c83f9432eb
Cleaned up RefMetaDataTracker
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Renamed many functions to more clearly state what they are actually doing
Removed unnecessary / unused functionality, reducing interface complexity
Updated all uses of this code in GATK
Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz)
Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding
2011-07-27 23:25:52 -04:00
1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
f3ad4ec94b
Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.
2011-07-27 22:06:23 -04:00
ff31fa7990
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 16:15:23 -04:00
5809a61b20
Merged bug fix from Stable into Unstable
2011-07-27 16:14:59 -04:00
Mark DePristo
David Roazen
Eric Banks
Ryan Poplin
Khalid Shakir
Guillermo del Angel