diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index e5144e9cd..1a6c9b8fd 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -19,6 +19,9 @@ import java.util.ArrayList; * To change this template use File | Settings | File Templates. */ public class PileupWalker extends LocusWalker { + @Argument(fullName="verbose",required=false,defaultValue="false") + public boolean VERBOSE; + public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument? public void initialize() { @@ -39,6 +42,12 @@ public class PileupWalker extends LocusWalker { bases = "*** UNCOVERED SITE ***"; } + String extras = ""; + if ( VERBOSE ) { + extras += " BQ=" + Utils.join(",", Utils.qualPileup(reads, offsets)); + extras += " MQ=" + Utils.join(",", Utils.mappingQualPileup(reads)); + } + String rodString = ""; for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) { if ( datum != null && ! (datum instanceof rodDbSNP)) { @@ -53,7 +62,7 @@ public class PileupWalker extends LocusWalker { rodString = "[ROD: " + rodString + "]"; //if ( context.getLocation().getStart() % 1 == 0 ) { - out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString); + out.printf("%s: %s %s %s%s %s%n", context.getLocation(), ref, bases, quals, extras, rodString); //} return 1;