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Fixed bugs in DiagnoseTargets 

DT would not report bad mates!
that has been fixed

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
This commit is contained in:
Roger Zurawicki 2012-06-12 16:49:52 -04:00 committed by Mauricio Carneiro
parent 538cdf9210
commit bdf5945dcc
3 changed files with 30 additions and 14 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
View File

@ -250,6 +250,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
private void outputStatsToVCF(IntervalStatistics stats, Allele refAllele) {
GenomeLoc interval = stats.getInterval();
List<Allele> alleles = new ArrayList<Allele>();
Map<String, Object> attributes = new HashMap<String, Object>();
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
@ -265,7 +266,9 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
attributes.put(VCFConstants.DEPTH_KEY, stats.averageCoverage());
vcb = vcb.attributes(attributes);
if (debug) {
System.out.printf("Output -- Interval: %s, Coverage: %.2f%n", stats.getInterval(), stats.averageCoverage());
}
for (String sample : samples) {
Map<String, Object> infos = new HashMap<String, Object>();
SampleStatistics sampleStat = stats.getSample(sample);
@ -277,14 +280,14 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
Set<String> filters = new HashSet<String>();
filters.addAll(statusesToStrings(stats.getSample(sample).getCallableStatuses(thresholds)));
if (debug) {
System.out.printf("Found %d bad mates out of %d reads %n", sampleStat.getnBadMates(), sampleStat.getnReads());
}
genotypes.add(new Genotype(sample, null, VariantContext.NO_LOG10_PERROR, filters, infos, false));
}
vcb = vcb.genotypes(genotypes);
if (debug) {
System.out.printf("Output -- Interval: %s, Coverage: %.2f%n", stats.getInterval(), stats.averageCoverage());
}
vcfWriter.add(vcb.make());
@ -306,6 +309,6 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
}
private IntervalStatistics createIntervalStatistic(GenomeLoc interval) {
return new IntervalStatistics(samples, interval /*, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality*/);
return new IntervalStatistics(samples, interval);
}
}

27
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
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@ -104,19 +104,19 @@ class SampleStatistics {
double intervalSize = interval.size();
if ((nBadMates / nReads) > thresholds.getBadMateStatusThreshold())
if (((double) nBadMates / nReads) >= thresholds.getBadMateStatusThreshold())
output.add(CallableStatus.BAD_MATE);
if ((totals.get(CallableStatus.COVERAGE_GAPS) / intervalSize) > thresholds.getCoverageStatusThreshold())
if ((totals.get(CallableStatus.COVERAGE_GAPS) / intervalSize) >= thresholds.getCoverageStatusThreshold())
output.add(CallableStatus.COVERAGE_GAPS);
if ((totals.get(CallableStatus.LOW_COVERAGE) / intervalSize) > thresholds.getCoverageStatusThreshold())
if ((totals.get(CallableStatus.LOW_COVERAGE) / intervalSize) >= thresholds.getCoverageStatusThreshold())
output.add(CallableStatus.LOW_COVERAGE);
if ((totals.get(CallableStatus.EXCESSIVE_COVERAGE) / intervalSize) > thresholds.getExcessiveCoverageThreshold())
if ((totals.get(CallableStatus.EXCESSIVE_COVERAGE) / intervalSize) >= thresholds.getExcessiveCoverageThreshold())
output.add(CallableStatus.EXCESSIVE_COVERAGE);
if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) > thresholds.getQualityStatusThreshold())
if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) >= thresholds.getQualityStatusThreshold())
output.add(CallableStatus.POOR_QUALITY);
if (totals.get(CallableStatus.REF_N) > 0)
@ -161,7 +161,7 @@ class SampleStatistics {
// Was this read already processed?
if (read.getTemporaryAttribute("checkedBadMate") == null) {
nReads++;
if (hasValidMate(read, thresholds))
if (!hasValidMate(read, thresholds))
nBadMates++;
read.setTemporaryAttribute("checkedBadMate", true);
}
@ -254,7 +254,7 @@ class SampleStatistics {
* reasonable insert size?
* inverted?
* same orientation?
* todo - same contig?
* same contig?
* is pair mapped?
* todo - is forced mate?
*
@ -264,6 +264,10 @@ class SampleStatistics {
if (!read.getReadPairedFlag())
return false;
// different contigs
if (read.getMateReferenceIndex() != read.getReferenceIndex())
return false;
// unmapped
if (read.getMateUnmappedFlag() || read.getReadUnmappedFlag())
return false;
@ -277,10 +281,19 @@ class SampleStatistics {
read.getAlignmentStart() < read.getMateAlignmentStart())
return false;
// TODO note: IGV uses a different alorithm for insert size, there should be a common util class that does this for you
// mates are too far apart
if (Math.abs(read.getAlignmentStart() - read.getMateAlignmentStart()) > thresholds.getMaximumInsertSize())
return false;
return true;
}
public int getnReads() {
return nReads;
}
public int getnBadMates() {
return nBadMates;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
View File

@ -129,12 +129,12 @@ class ThresHolder {
// INFO fields for overall data
headerLines.add(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
headerLines.add(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a lci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
// todo -- find the appropriate VCF constants
headerLines.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a lci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine("Q1", 1, VCFHeaderLineType.Float, "Lower Quartile of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("MED", 1, VCFHeaderLineType.Float, "Median of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("Q3", 1, VCFHeaderLineType.Float, "Upper Quartile of depth Distribution."));