zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added verbose option to show mapping qualities and base qualities as ints! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-14 00:54:48 +00:00
parent cc75e8f712
commit 794360c410
1 changed files with 10 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -19,6 +19,9 @@ import java.util.ArrayList;
* To change this template use File | Settings | File Templates.
*/
public class PileupWalker extends LocusWalker<Integer, Integer> {
@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<Integer, Integer> {
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<Integer, Integer> {
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;