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Forgot a dumb little System.out.println. You will be flooded with "This read will not be used." statements until, overwhelmed, you give in to my demands. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1874 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-19 16:13:48 +00:00
parent 225ef52973
commit 3d50c72d74
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -87,9 +87,9 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
// System.out.println("Base quality is: "+reads.get(r).getBaseQualities()[offsets.get(r)]); // System.out.println("Base quality is: "+reads.get(r).getBaseQualities()[offsets.get(r)]);
// System.out.println("Read base is: "+ (char) reads.get(r).getReadBases()[offsets.get(r)]); // System.out.println("Read base is: "+ (char) reads.get(r).getReadBases()[offsets.get(r)]);
// System.out.println("Pileup is: " + map.getPileup().getBases()); // System.out.println("Pileup is: " + map.getPileup().getBases());
if ( ! useRead(reads.get(r),offsets.get(r),ref) ) { // if ( ! useRead(reads.get(r),offsets.get(r),ref) ) {
System.out.println("Read will not be used."); // System.out.println("Read will not be used.");
} //}
} }
if ( useRead( reads.get(r), offsets.get(r), ref ) ) { if ( useRead( reads.get(r), offsets.get(r), ref ) ) {
updateTables( reads.get(r), offsets.get(r), map ); updateTables( reads.get(r), offsets.get(r), map );