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

View File

@ -116,21 +116,28 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
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) {
final StringBuilder sb = new StringBuilder();
boolean isFirst = true;
sb.append(pileup.getNumberOfDeletions());
sb.append(" ");
for ( PileupElement p : pileup ) {
if ( isFirst )
isFirst = false;
else
sb.append(",");
sb.append(p.getRead().getReadName());
sb.append(":");
sb.append(verboseDelimiter);
sb.append(p.getOffset());
sb.append(":");
sb.append(verboseDelimiter);
sb.append(p.getRead().getReadLength());
sb.append(verboseDelimiter);
sb.append(p.getRead().getMappingQuality());
}
return sb.toString();
}