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qualsAsInt argument for Pileup -- fixing stupid bug 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-04 18:51:17 +00:00
parent 9de3e58aa8
commit 97c8ff75dd
2 changed files with 5 additions and 2 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -86,6 +86,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
rodString = "[ROD: " + rodString + "]";
//if ( context.getLocation().getStart() % 1 == 0 ) {
System.out.printf("quals as ints %b%n", qualsAsInts);
out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
//}

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

@ -55,6 +55,7 @@ public class ReadBackedPileup extends BasicPileup {
}
public String getQualsAsInts() {
System.out.printf("getQualsAsInts");
return Utils.join(",", qualPileup(reads, offsets));
}
@ -83,12 +84,13 @@ public class ReadBackedPileup extends BasicPileup {
// 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.
System.out.printf("qualsAsInts %b%n", qualsAsInts);
//return String.format("%s %s %s %s", getLocation(), getRef(), getBases(), getQuals());
return String.format("%s %s %s %s %s %s",
getLocation().getContig(), getLocation().getStart(), // chromosome name and coordinate
getRef(), // reference base
getBases(),
qualsAsInts ? getQuals() : getQualsAsInts(),
qualsAsInts ? getMappingQuals() : getMappingQualsAsInts());
qualsAsInts ? getQualsAsInts() : getQuals(),
qualsAsInts ? getMappingQualsAsInts() : getMappingQuals() );
}
}