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deal with bad record #36

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Merged
bayolau merged 1 commit into from
Mar 20, 2017
Merged

deal with bad record #36

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11 changes: 10 additions & 1 deletion src/main/java/com/bina/lrsim/sam/SamAlignment.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,13 @@ public class SamAlignment implements EventGroup {

public SamAlignment(SAMRecord samRecord, ReferenceSequenceFile references) {
this.samRecord = samRecord;
load(this.samRecord, references);
try {
load(this.samRecord, references);
}
catch ( htsjdk.samtools.SAMException e ) {
log.error("bad alignment record:. " + e.getMessage());
pairwiseAlignment = null;
}
}

private static int getAlignmentLength(SAMRecord samRecord) {
Expand Down Expand Up @@ -56,6 +62,9 @@ public void load(SAMRecord samRecord, ReferenceSequenceFile references) {

int seqSamPos = 0;
int refRefPos = 0;
// log.info(samRecord.getReferenceName());
// log.info(samRecord.getAlignmentStart());
// log.info(samRecord.getAlignmentEnd());
final byte[] refRef = references.getSubsequenceAt(samRecord.getReferenceName(), samRecord.getAlignmentStart(), samRecord.getAlignmentEnd()).getBases();

int seqNext = 0;
Expand Down