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Better handling for case where PL attribute is missing. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@905 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-05 02:52:30 +00:00
parent 2035d7dfd3
commit fdfc3abf80
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
@ -107,6 +108,12 @@ 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();
@ -114,7 +121,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
for (int i =0; i < reads.size(); i++ ) { for (int i =0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
SAMReadGroupRecord readGroup = read.getHeader().getReadGroup((String)read.getAttribute("RG")); SAMReadGroupRecord readGroup = read.getHeader().getReadGroup((String)read.getAttribute("RG"));
if ( "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString()) && if ( readGroup.getAttribute("PL") == null || "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString()) &&
!read.getReadNegativeStrandFlag() && !read.getReadNegativeStrandFlag() &&
(READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) && (READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) &&
(read.getMappingQuality() >= MIN_MAPPING_QUALITY)) { (read.getMappingQuality() >= MIN_MAPPING_QUALITY)) {