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output to out... not System.out... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1034 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-06-17 20:43:10 +00:00
parent b947fd586f
commit 615572ea06
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
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@ -314,7 +314,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
" QSUM was " + tumorReadPile.qualitySums.get(altAllele) + " QSUM was " + tumorReadPile.qualitySums.get(altAllele) +
" QSUM is now " + t2.qualitySums.get(altAllele); " QSUM is now " + t2.qualitySums.get(altAllele);
System.out.println( out.println(
context.getContig() + "\t" + context.getContig() + "\t" +
context.getPosition() + "\t" + context.getPosition() + "\t" +
context.getPosition() + "\t" context.getPosition() + "\t"
@ -333,7 +333,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
if (OUTPUT_FAILURES) { if (OUTPUT_FAILURES) {
String msg = "FAILED due to DISALIGNMENT TEST."; String msg = "FAILED due to DISALIGNMENT TEST.";
System.out.println( out.println(
context.getContig() + "\t" + context.getContig() + "\t" +
context.getPosition() + "\t" + context.getPosition() + "\t" +
context.getPosition() + "\t" context.getPosition() + "\t"
@ -368,7 +368,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
"__NAltSum: " + normalReadPile.qualitySums.get(altAllele) + "__NAltSum: " + normalReadPile.qualitySums.get(altAllele) +
"__MIDP: " + midp.get(altAllele); "__MIDP: " + midp.get(altAllele);
System.out.println( out.println(
context.getContig() + "\t" + context.getContig() + "\t" +
context.getPosition() + "\t" + context.getPosition() + "\t" +
context.getPosition() + "\t" context.getPosition() + "\t"
@ -419,7 +419,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
char base = read.getReadString().charAt(offset); char base = read.getReadString().charAt(offset);
// TODO: use a logger to output this information for debugging/Picard folks // TODO: use a logger to output this information for debugging/Picard folks
//System.out.println("MMQSUM: Filtering out " + read.getReadName() + " with locus base " + base + " and ref of " + pile.refBase); //out.println("MMQSUM: Filtering out " + read.getReadName() + " with locus base " + base + " and ref of " + pile.refBase);
} }
} }
return newPile; return newPile;
@ -553,7 +553,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
if ( mismatchScore > 0 ) { if ( mismatchScore > 0 ) {
if ( mismatchScore > 100) { if ( mismatchScore > 100) {
System.out.println(read.getReadName() + " has a sum of mismatch quality scores of " + mismatchScore); out.println(read.getReadName() + " has a sum of mismatch quality scores of " + mismatchScore);
} else { } else {
altReads.add(aRead); altReads.add(aRead);