From f049461120b0f333964011a5e1ad20cc93f61992 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Sat, 6 Aug 2011 20:44:19 -0400 Subject: [PATCH] Changed @Argument to @Input on input RodBindings. Changed shortname collision with longname. Restored scala builds. Updated HSP to use new syntax. --- build.xml | 12 ++++++------ .../sting/gatk/walkers/PileupWalker.java | 3 ++- .../walkers/filters/VariantFiltrationWalker.java | 2 +- .../gatk/walkers/variantutils/SelectVariants.java | 4 ++-- .../java/test/org/broadinstitute/sting/BaseTest.java | 1 + 5 files changed, 12 insertions(+), 10 deletions(-) diff --git a/build.xml b/build.xml index 9af8949ba..438e9c90c 100644 --- a/build.xml +++ b/build.xml @@ -168,7 +168,7 @@ - + @@ -973,11 +973,11 @@ - - - - - + + + + diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index e998c8452..6243a6cc0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers; import org.broad.tribble.Feature; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -71,7 +72,7 @@ public class PileupWalker extends LocusWalker implements TreeR @Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events") public boolean SHOW_INDEL_PILEUPS = false; - @Argument(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false) + @Input(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false) public List> rods = Collections.emptyList(); public void initialize() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index d8e6ad227..0daabfa45 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -78,7 +78,7 @@ public class VariantFiltrationWalker extends RodWalker { @Argument(fullName="maskExtension", shortName="maskExtend", doc="How many bases beyond records from a provided 'mask' rod should variants be filtered; [default:0]", required=false) protected Integer MASK_EXTEND = 0; - @Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false) + @Argument(fullName="maskName", shortName="maskName", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false) protected String MASK_NAME = "Mask"; @Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 063b005a6..a74349727 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -82,10 +82,10 @@ public class SelectVariants extends RodWalker { @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false) private boolean KEEP_ORIGINAL_CHR_COUNTS = false; - @Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false) + @Input(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false) private RodBinding discordanceTrack = RodBinding.makeUnbound(VariantContext.class); - @Argument(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false) + @Input(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false) private RodBinding concordanceTrack = RodBinding.makeUnbound(VariantContext.class); @Hidden diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index e864e5754..a95f044ec 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -65,6 +65,7 @@ public abstract class BaseTest { public static final String dbsnpDataLocation = GATKDataLocation; public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf"; + public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf"; public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf"; public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";