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Adding error model header names in the BQSR recal plot. Making the downsampling of points look a little nicer.

This commit is contained in:
Ryan Poplin 2012-07-23 11:28:17 -04:00
parent 2e486d83e2
commit 10d143c35c
2 changed files with 11 additions and 7 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java
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@ -3,16 +3,18 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
public enum EventType { public enum EventType {
BASE_SUBSTITUTION(0, "M"), BASE_SUBSTITUTION(0, "M", "Base Substitution"),
BASE_INSERTION(1, "I"), BASE_INSERTION(1, "I", "Base Insertion"),
BASE_DELETION(2, "D"); BASE_DELETION(2, "D", "Base Deletion");
public final int index; public final int index;
private final String representation; private final String representation;
private final String longRepresentation;
private EventType(int index, String representation) { private EventType(int index, String representation, String longRepresentation) {
this.index = index; this.index = index;
this.representation = representation; this.representation = representation;
this.longRepresentation = longRepresentation;
} }
public static EventType eventFrom(int index) { public static EventType eventFrom(int index) {
@ -40,4 +42,8 @@ public enum EventType {
public String toString() { public String toString() {
return representation; return representation;
} }
public String prettyPrint() {
return longRepresentation;
}
} }

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
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@ -410,9 +410,7 @@ public class RecalDataManager {
final int covariateKey = (Integer)keys.get(2); final int covariateKey = (Integer)keys.get(2);
values.add(covariate.formatKey(covariateKey)); values.add(covariate.formatKey(covariateKey));
values.add(covariateNameMap.get(covariate)); values.add(covariateNameMap.get(covariate));
values.add(EventType.eventFrom((Integer)keys.get(3)).prettyPrint());
final EventType event = EventType.eventFrom((Integer)keys.get(3));
values.add(event);
return values; return values;
} }