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Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-14 13:58:28 +00:00
parent 998fad76c6
commit 30121534ed
1 changed files with 17 additions and 0 deletions
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17
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -44,6 +44,23 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
String extras = ""; String extras = "";
if ( VERBOSE ) { if ( VERBOSE ) {
String sqbases = Utils.secondaryBasePileupAsString(reads, offsets);
String sqquals = Utils.secondaryQualPileupAsString(reads, offsets);
if (sqbases != null && sqquals != null) {
assert(sqbases.length() == sqquals.length());
extras += " SQ=";
for (int i = 0; i < sqbases.length(); i++) {
extras += sqbases.charAt(i);
extras += sqquals.charAt(i);
if (i < sqbases.length() - 1) {
extras += ',';
}
}
}
extras += " BQ=" + Utils.join(",", Utils.qualPileup(reads, offsets)); extras += " BQ=" + Utils.join(",", Utils.qualPileup(reads, offsets));
extras += " MQ=" + Utils.join(",", Utils.mappingQualPileup(reads)); extras += " MQ=" + Utils.join(",", Utils.mappingQualPileup(reads));
} }