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Minor changes to verbose mode

This commit is contained in:
Eric Banks 2012-04-03 10:53:48 -04:00
parent 8ca4df38ed
commit f9ce9962c4
1 changed files with 10 additions and 3 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -117,20 +117,27 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
return rodString; return rodString;
} }
private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
private static String createVerboseOutput(final ReadBackedPileup pileup) { private static String createVerboseOutput(final ReadBackedPileup pileup) {
final StringBuilder sb = new StringBuilder(); final StringBuilder sb = new StringBuilder();
boolean isFirst = true; boolean isFirst = true;
sb.append(pileup.getNumberOfDeletions());
sb.append(" ");
for ( PileupElement p : pileup ) { for ( PileupElement p : pileup ) {
if ( isFirst ) if ( isFirst )
isFirst = false; isFirst = false;
else else
sb.append(","); sb.append(",");
sb.append(p.getRead().getReadName()); sb.append(p.getRead().getReadName());
sb.append(":"); sb.append(verboseDelimiter);
sb.append(p.getOffset()); sb.append(p.getOffset());
sb.append(":"); sb.append(verboseDelimiter);
sb.append(p.getRead().getReadLength()); sb.append(p.getRead().getReadLength());
sb.append(verboseDelimiter);
sb.append(p.getRead().getMappingQuality());
} }
return sb.toString(); return sb.toString();
} }