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Merged bug fix from Stable into Unstable

This commit is contained in:
Christopher Hartl 2011-11-09 11:06:15 -05:00
parent e1b4c3968f 091229e4db
commit 5451fbc2b2
3 changed files with 16 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -33,7 +33,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( mendelianViolation == null ) { if ( mendelianViolation == null ) {
if ( walker instanceof VariantAnnotator ) { if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP ); mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
} }
else { else {
@ -42,9 +42,9 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
} }
Map<String,Object> toRet = new HashMap<String,Object>(1); Map<String,Object> toRet = new HashMap<String,Object>(1);
boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) && boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) && vc.getGenotype(mendelianViolation.getSampleChild()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleDad()) && vc.hasGenotype(mendelianViolation.getSampleDad()) && vc.getGenotype(mendelianViolation.getSampleDad()).hasLikelihoods() &&
vc.hasGenotype(mendelianViolation.getSampleMom()); vc.hasGenotype(mendelianViolation.getSampleMom()) && vc.getGenotype(mendelianViolation.getSampleMom()).hasLikelihoods();
if ( hasAppropriateGenotypes ) if ( hasAppropriateGenotypes )
toRet.put("MVLR",mendelianViolation.violationLikelihoodRatio(vc)); toRet.put("MVLR",mendelianViolation.violationLikelihoodRatio(vc));

6
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
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@ -86,7 +86,13 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
public Object readHeader(LineReader reader) { public Object readHeader(LineReader reader) {
String line = ""; String line = "";
try { try {
boolean isFirst = true;
while ((line = reader.readLine()) != null) { while ((line = reader.readLine()) != null) {
System.out.println(line);
if ( isFirst && ! line.startsWith(headerDelimiter) ) {
throw new UserException.MalformedFile("TableCodec file does not have a header");
}
isFirst &= false;
if (line.startsWith(headerDelimiter)) { if (line.startsWith(headerDelimiter)) {
if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line); if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line);
String spl[] = line.split(delimiterRegex); String spl[] = line.split(delimiterRegex);

6
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
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@ -1,7 +1,9 @@
package org.broadinstitute.sting.utils.codecs.table; package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import java.util.List; import java.util.List;
@ -44,6 +46,10 @@ public class TableFeature implements Feature {
return values.get(columnPosition); return values.get(columnPosition);
} }
public String toString() {
return String.format("%s\t%s",position.toString(), Utils.join("\t",values));
}
public String get(String columnName) { public String get(String columnName) {
int position = keys.indexOf(columnName); int position = keys.indexOf(columnName);
if (position < 0) throw new IllegalArgumentException("We don't have a column named " + columnName); if (position < 0) throw new IllegalArgumentException("We don't have a column named " + columnName);