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Readded locus printing suppression to DoC walker 

(and removed unused import from UG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-15 14:50:56 +00:00
parent 0d2a761460
commit b234019cf5
2 changed files with 12 additions and 7 deletions
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18
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
View File

@ -43,13 +43,16 @@ import java.util.*;
@By(DataSource.REFERENCE)
public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoCInfo, DepthOfCoverageWalker.DoCInfo> {
@Argument(fullName="printBaseCounts", shortName = "bases", doc="Print individual base counts (A,C,G,T only)", required=false)
@Argument(fullName="suppressLocusPrinting", shortName= "noLocus", doc="Suppress printing", required=false)
public boolean suppressLocusPrinting = false;
@Argument(fullName="printBaseCounts", shortName ="bases", doc="Print individual base counts (A,C,G,T only)", required=false)
protected boolean printBaseCounts = false;
@Argument(fullName="minMAPQ", shortName = "minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
@Argument(fullName="minMAPQ", shortName ="minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
protected int excludeMAPQBelowThis = -1;
@Argument(fullName="minDepth", shortName = "minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
@Argument(fullName="minDepth", shortName ="minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
protected int minDepthForPercentage = -1;
@Argument(fullName="byReadGroup", shortName="byRG", doc="List read depths for each read group")
@ -99,8 +102,10 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
}
// build and print the per-locus header
out.println("\nPER_LOCUS_COVERAGE_SECTION");
printHeaderLine(false);
if ( !suppressLocusPrinting ) {
out.println("\nPER_LOCUS_COVERAGE_SECTION");
printHeaderLine(false);
}
}
public DoCInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@ -153,7 +158,8 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
if ( printHistogram )
incCov(info.totalCoverage);
printDoCInfo(context.getLocation(), info, false);
if ( !suppressLocusPrinting )
printDoCInfo(context.getLocation(), info, false);
return info;
}

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.genotype.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.alignment.Alignment;
import net.sf.samtools.SAMReadGroupRecord;