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Tool to manipulate intervals outside the GATK 

Performs basic set operations on intervals like union, intersect and difference between two or more intervals. Useful for techdev and QC purposes.
This commit is contained in:
Mauricio Carneiro 2013-05-02 13:41:25 -04:00
parent 3dbb86b052
commit 9eceae793a
2 changed files with 7 additions and 16 deletions
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19
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -65,8 +65,7 @@ import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.*;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.util.*;
/**
@ -200,11 +199,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
}
if (thresholds.missingTargets != null) {
try {
thresholds.missingTargets.close();
} catch (IOException e) {
e.printStackTrace();
}
thresholds.missingTargets.close();
}
}
@ -326,13 +321,9 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
}
}
private void outputMissingInterval(final String contig, final int start, final int stop){
final FileWriter out = thresholds.missingTargets;
try {
out.write(String.format("%s:%d-%d\n", contig, start, stop));
} catch (IOException e) {
e.printStackTrace();
}
private void outputMissingInterval(final String contig, final int start, final int stop) {
final PrintStream out = thresholds.missingTargets;
out.println(String.format("%s:%d-%d", contig, start, stop));
}
/**

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
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@ -49,7 +49,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import java.io.FileWriter;
import java.io.PrintStream;
import java.util.LinkedList;
import java.util.List;
@ -117,7 +117,7 @@ final class ThresHolder {
public double qualityStatusThreshold = 0.50;
@Output(fullName = "missing_intervals", shortName = "missing", doc ="Produces a file with the intervals that don't pass filters", required = false)
public FileWriter missingTargets = null;
public PrintStream missingTargets = null;
public final List<Metric> locusMetricList = new LinkedList<Metric>();
public final List<Metric> sampleMetricList = new LinkedList<Metric>();