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VariantsToTable now works with multiple input VCFs

This commit is contained in:
Mark DePristo 2012-04-02 09:13:35 -04:00
parent 8072060496
commit 6b7a00061a
1 changed files with 8 additions and 3 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -95,8 +95,13 @@ import java.util.*;
* @since 2010
*/
public class VariantsToTable extends RodWalker<Integer, Integer> {
@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<RodBinding<VariantContext>> variants;
@Output(doc="File to which results should be written",required=true)
protected PrintStream out;
@ -155,7 +160,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
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<String> record : extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA, splitMultiAllelic) )
out.println(Utils.join("\t", record));