9d2cda3d41
Removed a public -> private dependency in our test suite.
2011-08-12 17:29:10 -04:00
bb4ced3201
SnpEff-related fixes.
...
-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.
-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
2011-08-12 15:26:24 -04:00
10e873d9c6
Merge branch 'repval'
2011-08-12 15:24:31 -04:00
31dc831531
Merged bug fix from Stable into Unstable
2011-08-12 13:26:41 -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
7ea9196321
Better error message for name/type clashes.
2011-08-12 11:18:14 -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
90771b74b4
When matching eval to comps, try to choose the one with the same alt allele.
2011-08-11 13:55:01 -04:00
200f73b008
No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
2011-08-11 13:44:07 -04:00
e93538cdf7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 13:39:36 -04:00
265c3d744b
Fixing VariantEval logic and having it use the new rod system.
2011-08-11 13:39:34 -04:00
b705d9cf15
Oops, these VariantAnnotator input bindings aren't needed during the UG
2011-08-11 13:17:16 -04:00
7fade88070
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:02:47 -04:00
c7b9a9ef0a
Updating UnifiedGenotyper to use the new rod binding system.
2011-08-11 11:02:11 -04:00
418a4d541f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:01:38 -04:00
e71255d3c2
GATKDocsExample walker
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-- Shows the best practice for documentating a walker with the GATKdocs
-- See http://www.broadinstitute.org/gsa/wiki/index.php/GATKdocs#Writing_GATKdocs_for_your_walkers for a brief discussion
2011-08-11 11:01:21 -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.
...
-- 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
dd5fe8291d
Fixing up some comments in the BQSR
2011-08-11 08:36:00 -04:00
f1b09db39e
Fixes for rod bindings
2011-08-10 23:08:47 -04:00
75985c2fa0
Resolving merge conflicts
2011-08-10 22:45:11 -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
0086e27741
makeUnbound now package protected
...
-- Removed references to it in the codebase
-- Fixed documentation I saw that had the summary + body style
2011-08-10 22:29:32 -04:00
cb6cf25bb0
Updating SelectVariants documentation to reflect best practice
2011-08-10 22:24:18 -04:00
00b4d6ec57
Updated the best practice on documenting a field
...
-- Best practice is now to skip the summary, as this is the @annotation doc value.
2011-08-10 22:21:12 -04:00
2007d2fcad
Better documentation for default value fields
...
-- DocString function for types that create default outputs "stdout"
-- RodBinding now creates a makeUnbound default value automatically for you if your RodBinding isn't required
-- Removed warning about sparse help from TextFormattingUtils
2011-08-10 22:16:22 -04:00
bb557266ca
Merge branches to get new RodBinding framework
...
Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
2011-08-10 18:23:01 -04:00
8325cb8c26
Fixing up apparent source control/merge snafu: fix to correctly output PL ordering in multi-allelic sites by UG was only half-committed and hence not working. This completes fix
2011-08-10 15:31:49 -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
577f861f69
Pass the rodBindings into the VariantAnnotator engine, and from there to the
...
annotation classes themselves.
2011-08-10 13:11:57 -04:00
480e7a7984
Correctly initialize the optional SnpEff rod binding in VariantAnnotator using
...
RodBinding.makeUnbound()
2011-08-10 12:25:26 -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
c884b6bf1f
Fixed comment
2011-08-10 12:07:43 -04:00
06cdc4d5f9
Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.
2011-08-10 12:00:56 -04:00
bc125f104a
TrainingSets class is obsolete now.
2011-08-10 10:23:33 -04:00
David Roazen
Mauricio Carneiro
Guillermo del Angel
Menachem Fromer
Eric Banks
Ryan Poplin
Mark DePristo