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Cleaned up error warning in case no PL groups are present. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@907 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-05 03:14:17 +00:00
parent 45eeefbb80
commit 9da04fd9ac
1 changed files with 2 additions and 6 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -93,6 +93,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
public void initialize() { public void initialize() {
for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) { for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) {
if( readGroup.getAttribute("PL") == null )
Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId()));
data.put(readGroup.getReadGroupId(), new RecalData[MAX_READ_LENGTH+1][MAX_QUAL_SCORE+1][NDINUCS]); data.put(readGroup.getReadGroupId(), new RecalData[MAX_READ_LENGTH+1][MAX_QUAL_SCORE+1][NDINUCS]);
for ( int i = 0; i < MAX_READ_LENGTH+1; i++) { for ( int i = 0; i < MAX_READ_LENGTH+1; i++) {
for ( int j = 0; j < MAX_QUAL_SCORE+1; j++) { for ( int j = 0; j < MAX_QUAL_SCORE+1; j++) {
@ -108,12 +110,6 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
// No PL attribute? Warn the user and keep going.
for(SAMReadGroupRecord readGroup: getToolkit().getEngine().getSAMHeader().getReadGroups()) {
if( readGroup.getAttribute("PL") == null )
Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId()));
}
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
if ( dbsnp == null || !dbsnp.isSNP() ) { if ( dbsnp == null || !dbsnp.isSNP() ) {
List<SAMRecord> reads = context.getReads(); List<SAMRecord> reads = context.getReads();