From 6b7a00061a977d828cca3053df22a984bc8af7a5 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 2 Apr 2012 09:13:35 -0400 Subject: [PATCH] VariantsToTable now works with multiple input VCFs --- .../gatk/walkers/variantutils/VariantsToTable.java | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 4c8e8df5c..46a3ba39c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -95,8 +95,13 @@ import java.util.*; * @since 2010 */ public class VariantsToTable extends RodWalker { - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + /** + * Variants from this VCF file are used by this tool as input. + * The file must at least contain the standard VCF header lines, but + * can be empty (i.e., no variants are contained in the file). + */ + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) + public List> variants; @Output(doc="File to which results should be written",required=true) protected PrintStream out; @@ -155,7 +160,7 @@ public class VariantsToTable extends RodWalker { if ( tracker == null ) // RodWalkers can make funky map calls return 0; - for ( VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) { + for ( VariantContext vc : tracker.getValues(variants, context.getLocation())) { if ( showFiltered || vc.isNotFiltered() ) { for ( final List record : extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA, splitMultiAllelic) ) out.println(Utils.join("\t", record));