b3b9b74d2cgot rid of the useless parameter classes
Mauricio Carneiro
2011-08-12 14:21:30 -0400
31dc831531Merged bug fix from Stable into Unstable
Guillermo del Angel
2011-08-12 13:26:41 -0400
9121b8ed65Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2011-08-12 12:24:19 -0400
7ed120361dFixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
Menachem Fromer
2011-08-12 12:23:44 -0400
7ea9196321Better error message for name/type clashes.
Eric Banks
2011-08-12 11:18:14 -0400
27f0748b33Renaming 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).
Eric Banks
2011-08-12 11:11:56 -0400
f5b2cc4977I'm really starting to hate this pipeline test.
Eric Banks
2011-08-12 10:45:58 -0400
005bd71be3Working too quickly earlier. Fixing syntax.
Eric Banks
2011-08-12 10:29:36 -0400
c7ca33cbffMerge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2011-08-12 10:12:09 -0400
639a01f382Updating integration test now that VE has been updated
Eric Banks
2011-08-12 07:15:08 -0400
41f3da75d7Implementation 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.
Eric Banks
2011-08-12 02:22:44 -0400
45f973ab1fMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-08-12 00:40:18 -0400
eba316621dFinish 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. :)
Eric Banks
2011-08-12 00:40:08 -0400
6ee8a3a8ddFixing the javadoc/scaladoc targets in build.xml
David Roazen
2011-08-11 19:19:25 -0400
9de06560dfUpdate to new RodBinding system
Menachem Fromer
2011-08-11 17:54:16 -0400
f408d5ea93Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-08-11 17:04:18 -0400
f1d1252be2Fixing syntax of BQSR and UG performance tests.
Ryan Poplin
2011-08-11 17:04:09 -0400
bd5cdb8a43The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml
David Roazen
2011-08-11 16:38:29 -0400
902eb0c61eAdding dbsnp annotation back into the UG integration tests
Ryan Poplin
2011-08-11 13:55:03 -0400
90771b74b4When matching eval to comps, try to choose the one with the same alt allele.
Eric Banks
2011-08-11 13:55:01 -0400
200f73b008No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
Eric Banks
2011-08-11 13:44:07 -0400
e93538cdf7Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-08-11 13:39:36 -0400
265c3d744bFixing VariantEval logic and having it use the new rod system.
Eric Banks
2011-08-11 13:39:34 -0400
b705d9cf15Oops, these VariantAnnotator input bindings aren't needed during the UG
Ryan Poplin
2011-08-11 13:17:16 -0400
7fade88070Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-08-11 11:02:47 -0400
c7b9a9ef0aUpdating UnifiedGenotyper to use the new rod binding system.
Ryan Poplin
2011-08-11 11:02:11 -0400
418a4d541fMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-08-11 11:01:38 -0400
e71255d3c2GATKDocsExample walker
Mark DePristo
2011-08-11 11:01:21 -0400
79c86e211fMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-08-11 09:59:20 -0400
ea42ee4a95Updating BQSR for the new rod binding system.
Ryan Poplin
2011-08-11 09:58:42 -0400
8cdc0cbd9cMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-08-11 08:58:49 -0400
40e06f9afbFixed broken RodBinding defaults.
Mark DePristo
2011-08-11 08:58:30 -0400
dd5fe8291dFixing up some comments in the BQSR
Ryan Poplin
2011-08-11 08:36:00 -0400
f1b09db39eFixes for rod bindings
Eric Banks
2011-08-10 23:08:47 -0400
75985c2fa0Resolving merge conflicts
Eric Banks
2011-08-10 22:45:11 -0400
bdb1da30fdBetter interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.
Eric Banks
2011-08-10 22:43:08 -0400
8a0338c7b7Fixed broken documentationtest
Mark DePristo
2011-08-10 22:40:17 -0400
0086e27741makeUnbound now package protected
Mark DePristo
2011-08-10 22:29:32 -0400
cb6cf25bb0Updating SelectVariants documentation to reflect best practice
Mark DePristo
2011-08-10 22:24:18 -0400
b984b7aa9bMissing default values are now NA
Mark DePristo
2011-08-10 22:22:57 -0400
00b4d6ec57Updated the best practice on documenting a field
Mark DePristo
2011-08-10 22:21:12 -0400
2007d2fcadBetter documentation for default value fields
Mark DePristo
2011-08-10 22:16:22 -0400
e3f93413ecfixed a few null pointers
Mauricio Carneiro
2011-08-10 19:20:07 -0400
fabfa74904poolcaller now complies with new rodbinding system
Mauricio Carneiro
2011-08-10 18:38:45 -0400
bb557266caMerge branches to get new RodBinding framework
Mauricio Carneiro
2011-08-10 18:23:01 -0400
46051c36c6Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Mauricio Carneiro
2011-08-10 16:57:34 -0400
b0ff5b1ff7a better name for the pacbio processing pipeline
Mauricio Carneiro
2011-08-10 16:16:53 -0400
8325cb8c26Fixing 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
Guillermo del Angel
2011-08-10 15:31:49 -0400
07ad8c78a9More 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.
Eric Banks
2011-08-10 14:24:40 -0400
8d14d32a62Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-08-10 13:42:37 -0400
749c8bfbcdMoving more tools over to the new rod system
Eric Banks
2011-08-10 13:42:35 -0400
0497170bc9SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.
David Roazen
2011-08-10 12:56:31 -0400
577f861f69Pass the rodBindings into the VariantAnnotator engine, and from there to the annotation classes themselves.
David Roazen
2011-08-10 11:39:41 -0400
480e7a7984Correctly initialize the optional SnpEff rod binding in VariantAnnotator using RodBinding.makeUnbound()
David Roazen
2011-08-09 16:30:08 -0400
a42f90db11Moving 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.
Eric Banks
2011-08-10 12:20:18 -0400
c884b6bf1fFixed comment
Eric Banks
2011-08-10 12:07:43 -0400
06cdc4d5f9Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.
Eric Banks
2011-08-10 12:00:56 -0400
bc125f104aTrainingSets class is obsolete now.
Ryan Poplin
2011-08-10 10:23:33 -0400
60639e5aa5Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-08-10 10:20:57 -0400
c60cf52f73Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.
Ryan Poplin
2011-08-10 10:20:37 -0400
274006c1f9Expected values now reflect better VariantEval Novelty calculation
Mark DePristo
2011-08-10 09:15:52 -0400
9e53fd6880Fixed VCFGatherFunction to not provide incorrect rod_priority_list
Mark DePristo
2011-08-10 07:28:35 -0400
1ea5ec276bMinor cleanup
Eric Banks
2011-08-09 23:28:59 -0400
bc2d4f554dBringing Indel Realigner up to speed with the new rod binding syntax; now use -known to specify the known indels track.
Eric Banks
2011-08-09 23:21:17 -0400
b8f572b571Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-08-09 23:19:51 -0400
08631546c8Partial 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?
Eric Banks
2011-08-09 23:19:40 -0400
86afe878a7ReducedRead optimization: single pass likelihood calculation
Mark DePristo
2011-08-09 20:55:15 -0400
afd0b5b383Hybrid selection pipeline fix
Mark DePristo
2011-08-09 20:46:07 -0400
5f8264dddbRMS calculation protected again n == 0 bug
Mark DePristo
2011-08-09 20:44:27 -0400
2af206b0ae.variant not .variants
Mark DePristo
2011-08-09 19:58:10 -0400
489e5cffc1Missed a few 'variants'
Eric Banks
2011-08-09 14:29:15 -0400
5a3c99b7b9Fixing 'variants' change in qscript
Eric Banks
2011-08-09 12:30:46 -0400
c3c9876391Move reference to .rods away from symlinks in preparation for their going away in GATK 1.2
Eric Banks
2011-08-09 12:20:50 -0400
b20c4d5286Thanks 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.
Eric Banks
2011-08-09 12:04:55 -0400
78aa6db076added the 'reference' header line too. We are now header-compliant for vcf4.1.
Eric Banks
2011-08-09 11:45:54 -0400
ec76bf6d4aVCF headers now include 'contig' lines describing the name, length, and assembly (when easily parsable) for each contig in the reference.
Eric Banks
2011-08-09 11:24:48 -0400
7afb5c9f1cMore updates to be consistent with the new rod syntax.
Eric Banks
2011-08-09 10:11:37 -0400
1e490e0decBringing up to speed with new syntax
Eric Banks
2011-08-09 09:26:06 -0400
70b3daf689VariantsToVCF is up and running again; integration tests are reenabled (and added one for dbSNP).ant
Eric Banks
2011-08-09 03:03:43 -0400
cb28875c2aUpdated rod binding syntax usage on CombineVariants from .rodBind to .variants.
Khalid Shakir
2011-08-09 00:46:39 -0400
d15852be0aMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Mauricio Carneiro
2011-08-09 00:04:59 -0400
2db6225c53A read filter that sets all mapping qualities to a given value
Mauricio Carneiro
2011-08-09 00:04:42 -0400
2efa376619Made the necessary changes to get SnpEff support working with the new rodbinding system.
David Roazen
2011-08-08 23:23:42 -0400
b180a1311aMerge branch 'snpEff'
David Roazen
2011-08-08 22:12:14 -0400
28d8c8fcbcModified the SnpEff integration test to run on a much smaller interval.
David Roazen
2011-08-08 21:07:13 -0400
a13bc7b929Added an integration test for the SnpEff annotation support, as well as some extra safety checks and comments.
David Roazen
2011-08-08 20:01:24 -0400
80924d24deSingle positional arguments are now treated as names unless they actually match a tribble feature
Mark DePristo
2011-08-08 19:26:27 -0400
f8a56bc64bMerge branch 'master' into rodRefactor
Mark DePristo
2011-08-08 16:58:18 -0400
Mauricio Carneiro
Mark DePristo
David Roazen
Eric Banks
Guillermo del Angel
Menachem Fromer
Ryan Poplin
Khalid Shakir