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Adding a new getter in VariantsToTable to extract the indel event length.

This commit is contained in:
Ryan Poplin 2011-10-17 14:34:52 -04:00
parent 2193da6bfb
commit 6b02354d84
1 changed files with 9 additions and 1 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -294,6 +295,14 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
return x.toString();
}
});
getters.put("EVENTLENGTH", new Getter() { public String get(VariantContext vc) {
int maxLength = 0;
for ( final Allele a : vc.getAlternateAlleles() ) {
final int length = a.length() - vc.getReference().length();
if( Math.abs(length) > Math.abs(maxLength) ) { maxLength = length; }
}
return Integer.toString(maxLength);
}});
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
if ( vc.isSNP() && vc.isBiallelic() )
@ -304,7 +313,6 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });