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Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-21 22:27:26 +00:00
parent dac76f041b
commit 5abfc7d079
1 changed files with 8 additions and 16 deletions
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24
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -25,6 +25,9 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName="verbose",required=false,defaultValue="false") @Argument(fullName="verbose",required=false,defaultValue="false")
public boolean VERBOSE; public boolean VERBOSE;
@Argument(fullName="extended",shortName="ext",required=false,defaultValue="false")
public boolean EXTENDED;
public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument? public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument?
public void initialize() { public void initialize() {
@ -47,22 +50,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
if ( VERBOSE ) { if ( VERBOSE ) {
extras += " BQ=" + pileup.getQualsAsInts(); extras += " BQ=" + pileup.getQualsAsInts();
extras += " MQ=" + pileup.getMappingQualsAsInts(); extras += " MQ=" + pileup.getMappingQualsAsInts();
String sqbases = pileup.getSecondaryBasePileup();
String sqquals = pileup.getSecondaryQualPileup();
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 += ',';
}
}
}
} }
String rodString = ""; String rodString = "";
@ -85,6 +72,11 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
out.printf("%s%s %s%n", pileup.getPileupString(), extras, rodString); out.printf("%s%s %s%n", pileup.getPileupString(), extras, rodString);
//} //}
if ( EXTENDED ) {
String probDists = pileup.getProbDistPileup();
System.out.println(probDists);
}
return 1; return 1;
} }