import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
+import htsjdk.samtools.SAMFormatException;
import htsjdk.samtools.SAMRecord;
+import jalview.bin.Cache;
public class CigarParser
{
do
{
// check extent of read
- SAMRecord rec = it.next();
+ SAMRecord rec = null;
+ try {
+ rec = it.next();
+ } catch (SAMFormatException ex)
+ {
+ Cache.log.info("Bailing on parsing SAM File - see error below",ex);
+ break;
+ }
if (extent != null)
{