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
Ryan Poplin
Mark DePristo
Eric Banks
David Roazen
Khalid Shakir