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I was adding verbose output to the Pileup output for a one-off and decided that I might as well commit it as an option. Updated deprecated calls while I was in there.

This commit is contained in:
Eric Banks 2012-03-27 11:09:03 -05:00
parent a638996fe2
commit c112e0824a
1 changed files with 26 additions and 1 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -68,6 +69,9 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
@Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
public boolean SHOW_INDEL_PILEUPS = false;
@Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
public boolean SHOW_VERBOSE = false;
@Input(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
public List<RodBinding<Feature>> rods = Collections.emptyList();
@ -82,7 +86,10 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
if ( context.hasBasePileup() ) {
ReadBackedPileup basePileup = context.getBasePileup();
out.printf("%s %s%n", basePileup.getPileupString(ref.getBaseAsChar()), rods);
out.printf("%s %s", basePileup.getPileupString((char)ref.getBase()), rods);
if ( SHOW_VERBOSE )
out.printf(" %s", createVerboseOutput(basePileup));
out.println();
}
if ( context.hasExtendedEventPileup() ) {
@ -125,6 +132,24 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
return rodString;
}
private static String createVerboseOutput(final ReadBackedPileup pileup) {
final StringBuilder sb = new StringBuilder();
boolean isFirst = true;
for ( PileupElement p : pileup ) {
if ( isFirst )
isFirst = false;
else
sb.append(",");
sb.append(p.getRead().getReadName());
sb.append(":");
sb.append(p.getOffset());
sb.append(":");
sb.append(p.getRead().getReadLength());
}
return sb.toString();
}
@Override
public void onTraversalDone(Integer result) {