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

Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-26 15:58:21 +00:00
parent 008d677bea
commit 54bb643d19
1 changed files with 5 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
View File

@ -27,7 +27,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
Pileup truePileup = getTruePileup( tracker ); Pileup truePileup = getTruePileup( tracker );
if ( truePileup == null ) { if ( truePileup == null ) {
System.out.printf("No truth pileup data available at %s%n", pileup.getPileupString()); out.printf("No truth pileup data available at %s%n", pileup.getPileupString());
if ( ! CONTINUE_AFTER_AN_ERROR ) { if ( ! CONTINUE_AFTER_AN_ERROR ) {
Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases", Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
context.getLocation(), pileup.getBases())); context.getLocation(), pileup.getBases()));
@ -68,6 +68,10 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
*/ */
private Pileup getTruePileup( RefMetaDataTracker tracker ) { private Pileup getTruePileup( RefMetaDataTracker tracker ) {
rodSAMPileup pileup = (rodSAMPileup)tracker.lookup("pileup", null); rodSAMPileup pileup = (rodSAMPileup)tracker.lookup("pileup", null);
if( pileup == null )
return null;
if( pileup.hasPointGenotype() ) if( pileup.hasPointGenotype() )
return (Pileup)pileup.getPointGenotype(); return (Pileup)pileup.getPointGenotype();
else if( pileup.hasIndelGenotype() ) else if( pileup.hasIndelGenotype() )