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Now creates GATKSamRecords now SamRecords

This commit is contained in:
Mark DePristo 2011-10-19 17:49:17 -04:00
parent 52345f0aec
commit bba69701b5
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
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@ -146,7 +146,7 @@ public class ArtificialSAMUtils {
if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart);
SAMRecord record = new SAMRecord(header);
SAMRecord record = new GATKSamRecord(header);
record.setReadName(name);
record.setReferenceIndex(refIndex);
record.setAlignmentStart(alignmentStart);