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qualsAsInt argument for Pileup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-04 18:37:39 +00:00
parent 4d654f30d4
commit 9de3e58aa8
2 changed files with 6 additions and 4 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -35,6 +35,8 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false)
public boolean showSecondBaseQuals = false;
@Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false)
public boolean qualsAsInts = false;
@Argument(fullName="extended",shortName="ext",doc="extended",required=false)
public boolean EXTENDED = false;
@ -84,7 +86,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
rodString = "[ROD: " + rodString + "]";
//if ( context.getLocation().getStart() % 1 == 0 ) {
out.printf("%s%s %s%n", pileup.getPileupString(), extras, rodString);
out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
//}
if ( EXTENDED ) {

6
java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
View File

@ -78,7 +78,7 @@ public class ReadBackedPileup extends BasicPileup {
return probDistPileupAsString(reads, offsets);
}
public String getPileupString()
public String getPileupString(boolean qualsAsInts)
{
// In the pileup format, each line represents a genomic position, consisting of chromosome name,
// coordinate, reference base, read bases, read qualities and alignment mapping qualities.
@ -88,7 +88,7 @@ public class ReadBackedPileup extends BasicPileup {
getLocation().getContig(), getLocation().getStart(), // chromosome name and coordinate
getRef(), // reference base
getBases(),
getQuals(),
getMappingQuals());
qualsAsInts ? getQuals() : getQualsAsInts(),
qualsAsInts ? getMappingQuals() : getMappingQualsAsInts());
}
}