X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarParser.java;h=113223dfa1f72317dceb68a86893c08315df93b7;hb=refs%2Fheads%2Ffeatures%2FJAL-2909_bamImport_2_11_2;hp=a42c2b1eea4be5b467356391cf30f59b04966bd7;hpb=3f60a0d59ec67599e75d55055e8aaf7576020d07;p=jalview.git

diff --git a/src/jalview/datamodel/CigarParser.java b/src/jalview/datamodel/CigarParser.java
index a42c2b1..113223d 100644
--- a/src/jalview/datamodel/CigarParser.java
+++ b/src/jalview/datamodel/CigarParser.java
@@ -9,7 +9,9 @@ import java.util.TreeMap;
 
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
+import htsjdk.samtools.SAMFormatException;
 import htsjdk.samtools.SAMRecord;
+import jalview.bin.Cache;
 
 public class CigarParser
 {
@@ -291,7 +293,14 @@ 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)
       {