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
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
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-- 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
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-- 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
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-- 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
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
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annotation classes themselves.
2011-08-10 13:11:57 -04:00
480e7a7984
Correctly initialize the optional SnpEff rod binding in VariantAnnotator using
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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
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
b8f572b571
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-09 23:19:51 -04:00
08631546c8
Partial commit for David so he can see what I want to do with the VariantAnnotator. Added a DbsnpArgumentCollection that people can use in their walkers to ensure that we have a standard syntax whenever allowing dbsnp rods. Added it to UG, but didn't hook it up. Maybe we should do the same for the 'variant' rod?
2011-08-09 23:19:40 -04:00
86afe878a7
ReducedRead optimization: single pass likelihood calculation
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-- Low level add() now takes a nObs argument and rather than += likelihood now does += nObs * likelihood
2011-08-09 20:55:15 -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
78aa6db076
added the 'reference' header line too. We are now header-compliant for vcf4.1.
2011-08-09 11:45:54 -04:00
ec76bf6d4a
VCF headers now include 'contig' lines describing the name, length, and assembly (when easily parsable) for each contig in the reference.
2011-08-09 11:24:48 -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
d15852be0a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-09 00:04:59 -04:00
2db6225c53
A read filter that sets all mapping qualities to a given value
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Pacbio has decided to assign 255 to the MQ of all their reads since they claim their aligner does not produce a number equivalent to a mapping quality. Despite much back and forth, they are dead set on not using this field, so if we want to use their bams, we will need to override that. This filter does just that. Replacing all values with a given one. Default is 60.
2011-08-09 00:04:42 -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
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
Ryan Poplin
Mark DePristo
Eric Banks
David Roazen
Mauricio Carneiro