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VariantEval can now see the EvaluationContext group objects, so they can decide if/when to print interesting sites. GenotypeConcordance has a hard-coded option to print FNs that is on the way to being generally useful. VCFWriter now uses the US locale for formatting floating point numbers; I believe this fixes a long-standing annoyance. Italian guys will check on this. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3864 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-07-23 17:16:50 +00:00
parent 77cace3aff
commit 33090629ea
5 changed files with 29 additions and 7 deletions
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3
java/src/org/broad/tribble/vcf/VCFConstants.java
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@ -25,7 +25,10 @@
package org.broad.tribble.vcf;
import java.util.Locale;
public final class VCFConstants {
public static final Locale VCF_LOCALE = Locale.US;
// standard INFO/FORMAT field keys
public static final String ANCESTRAL_ALLELE_KEY = "AA";

11
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -38,6 +38,8 @@ import java.util.*;
@Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
public class GenotypeConcordance extends VariantEvaluator {
private static final boolean PRINT_INTERESTING_SITES = false;
protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);
// a mapping from allele count to stats
@ -58,6 +60,7 @@ public class GenotypeConcordance extends VariantEvaluator {
private static final int MAX_MISSED_VALIDATION_DATA = 100;
private VariantEvalWalker.EvaluationContext group = null;
static class FrequencyStats implements TableType {
class Stats {
@ -229,7 +232,9 @@ public class GenotypeConcordance extends VariantEvaluator {
private boolean warnedAboutValidationData = false;
public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
this.group = group;
String interesting = null;
// sanity check that we at least have either eval or validation data
@ -287,7 +292,6 @@ public class GenotypeConcordance extends VariantEvaluator {
truth = Genotype.Type.NO_CALL;
} else {
truth = validation.getGenotype(sample).getType();
// TODO -- capture "interesting" sites here, for example:
// interesting = "ConcordanceStatus=FP";
}
@ -301,6 +305,9 @@ public class GenotypeConcordance extends VariantEvaluator {
for (final String sample : validation.getSampleNames()) {
final Genotype.Type truth = validation.getGenotype(sample).getType();
sampleStats.incrValue(sample, truth, called);
if ( (truth == Genotype.Type.HOM_VAR || truth == Genotype.Type.HET) && called == Genotype.Type.NO_CALL ) {
if ( PRINT_INTERESTING_SITES ) System.out.printf("%s: HM3 FN => %s%n", group, validation);
}
}
}

8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -201,7 +201,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
// --------------------------------------------------------------------------------------------------------------
/** private class holding all of the information about a single evaluation group (e.g., for eval ROD) */
private class EvaluationContext implements Comparable<EvaluationContext> {
public class EvaluationContext implements Comparable<EvaluationContext> {
// useful for typing
public String evalTrackName, compTrackName, novelty, filtered;
public boolean enableInterestingSiteCaptures = false;
@ -221,6 +221,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
return Utils.join(CONTEXT_SEPARATOR, Arrays.asList(evalTrackName, compTrackName, selectExp == null ? "all" : selectExp.name, filtered, novelty));
}
public String toString() { return getDisplayName(); }
public int compareTo(EvaluationContext other) {
return this.getDisplayName().compareTo(other.getDisplayName());
}
@ -495,7 +497,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
switch ( evaluation.getComparisonOrder() ) {
case 1:
if ( evalWantsVC && vc != null ) {
String interesting = evaluation.update1(vc, tracker, ref, context);
String interesting = evaluation.update1(vc, tracker, ref, context, group);
if ( interesting != null ) interestingReasons.add(interesting);
}
break;
@ -506,7 +508,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
comp.hasNegLog10PError() &&
comp.getNegLog10PError() < (minCompQualScore / 10.0) )
comp = null;
String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context );
String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context, group );
if ( interesting != null ) interestingReasons.add(interesting);
break;
default:

10
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java
View File

@ -59,10 +59,20 @@ abstract class VariantEvaluator {
return null;
}
public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
return update1(vc1, tracker, ref, context);
}
public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return null;
}
public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
return update2(vc1, vc2, tracker, ref, context);
}
/**
* override this method for any finalization of calculations after the analysis is completed
*/

4
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
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@ -239,7 +239,7 @@ public class VCFWriter {
}
private String getQualValue(double qual) {
String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
String s = String.format(VCFConstants.VCF_LOCALE, VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) )
s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length());
return s;
@ -387,7 +387,7 @@ public class VCFWriter {
if ( val == null )
result = VCFConstants.MISSING_VALUE_v4;
else if ( val instanceof Double )
result = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
result = String.format(VCFConstants.VCF_LOCALE, VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
else if ( val instanceof Boolean )
result = (Boolean)val ? "" : null; // empty string for true, null for false
else if ( val instanceof List ) {