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
f0ee789a99
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-08 16:25:43 -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where it was combining Variant Contexts with different alternate alleles: if any of the genotypes had PLs they were no longer valid/correct.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
9756c1d7d7
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-08 14:16:31 -04:00
221b71c5a4
add 2nd round of counting covariates
2011-08-08 14:16:16 -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
1a0e5ab4ba
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-08 13:08:25 -04:00
a06f341685
qscript to assess BQSR known sets
2011-08-08 13:08:17 -04:00
99e3a72343
Merged bug fix from Stable into Unstable
2011-08-08 12:36:17 -04:00
8072bd9831
Updating resource bundle generation qscript for changeover to git
2011-08-08 12:35:39 -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
0db46d0648
Merged bug fix from Stable into Unstable
2011-08-08 10:50:09 -04:00
2fd101135c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-08 10:49:43 -04:00
4d6cb33612
removing temporary bam index
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The clean bai file was left behind after the data processing pipeline was done
2011-08-08 10:49:28 -04:00
e5fde0d16b
Merge branch 'master' into rodRefactor
2011-08-08 10:08:43 -04:00
88061ed5fa
rmdir the empty tmp dir if possible
2011-08-08 09:18:20 -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
738e94efcb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-07 17:36:45 -04:00
b3e57c329a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-07 15:18:15 -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
3c7a96cf2d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-07 12:12:47 -04:00
be0fc8a1e0
Now creates .gz archive of s3 downloads
2011-08-07 12:11:50 -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
f534c2e7bb
Merged bug fix from Stable into Unstable
2011-08-06 10:43:52 -04:00
eaa2f16d83
When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED.
2011-08-06 10:42:04 -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
b22a3d6508
Functional VCF output.
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It is outputting a VCF with the 'second best guess' for the alternate allele correctly. Annotations are added at the pool level, but may get overwritten at the lane and site level. Still need to implement the merging of the the annotations at higher levels.
2011-08-04 17:49:08 -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
Mark DePristo
David Roazen
Eric Banks
Ryan Poplin
Mauricio Carneiro
Khalid Shakir
Guillermo del Angel