Minor changes to verbose mode
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@ -116,21 +116,28 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
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return rodString;
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}
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private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
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private static String createVerboseOutput(final ReadBackedPileup pileup) {
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final StringBuilder sb = new StringBuilder();
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boolean isFirst = true;
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sb.append(pileup.getNumberOfDeletions());
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sb.append(" ");
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for ( PileupElement p : pileup ) {
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if ( isFirst )
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isFirst = false;
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else
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sb.append(",");
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sb.append(p.getRead().getReadName());
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sb.append(":");
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sb.append(verboseDelimiter);
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sb.append(p.getOffset());
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sb.append(":");
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sb.append(verboseDelimiter);
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sb.append(p.getRead().getReadLength());
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sb.append(verboseDelimiter);
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sb.append(p.getRead().getMappingQuality());
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}
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return sb.toString();
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}
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