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Don't print debugging output. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4799 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-06 20:57:11 +00:00
parent c91712bd59
commit bc885b7bd0
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
View File

@ -243,7 +243,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
*/ */
public void addAlignment( SAMRecord alignment ) { public void addAlignment( SAMRecord alignment ) {
if ( engine.getArguments().BAQMode != BAQ.CalculationMode.NONE && engine.getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_OUTPUT ) { if ( engine.getArguments().BAQMode != BAQ.CalculationMode.NONE && engine.getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_OUTPUT ) {
System.out.printf("Writing BAQ at OUTPUT TIME%n"); //System.out.printf("Writing BAQ at OUTPUT TIME%n");
baqHMM.baqRead(alignment, engine.getReferenceDataSource().getReference(), engine.getArguments().BAQMode, engine.getWalkerBAQQualityMode()); baqHMM.baqRead(alignment, engine.getReferenceDataSource().getReference(), engine.getArguments().BAQMode, engine.getWalkerBAQQualityMode());
} }

2
java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
View File

@ -38,7 +38,7 @@ public class BAQSamIterator implements StingSAMIterator {
} }
public SAMRecord next() { public SAMRecord next() {
System.out.printf("BAQing during input%n"); //System.out.printf("BAQing during input%n");
SAMRecord read = it.next(); SAMRecord read = it.next();
baqHMM.baqRead(read, refReader, cmode, qmode); baqHMM.baqRead(read, refReader, cmode, qmode);
return read; return read;