Catch samtools exceptions and make them 'BAM Exceptions' asking the user to run Picard's validator and re-index the file before posting anything to the forum. Let's see whether this helps or not.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5658 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -385,6 +385,25 @@ public abstract class CommandLineProgram {
         System.exit(1);
     }
 
+    public static void exitSystemWithSamError(final Exception e) {
+        if ( e.getMessage() == null )
+            throw new ReviewedStingException("SamException found with no message!", e);
+
+        errorPrintf("------------------------------------------------------------------------------------------%n");
+        errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
+        errorPrintf("The invalid inputs must be corrected before the GATK can proceed%n");
+        errorPrintf("Please do not post this error to the GATK forum until you have followed the instructions below%n");
+        errorPrintf("%n");
+        errorPrintf("Please make sure that your BAM file is well-formed by running Picard's validator on it%n");
+        errorPrintf("(see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)%n");
+        errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
+        printDocumentationReference();
+        errorPrintf("%n");
+        errorPrintf("MESSAGE: %s%n", e.getMessage().trim());
+        errorPrintf("------------------------------------------------------------------------------------------%n");
+        System.exit(1);
+    }
+
 
     /**
      * used to indicate an error occured

java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -92,6 +92,9 @@ public class CommandLineGATK extends CommandLineExecutable {
             // We can generate Tribble Exceptions in weird places when e.g. VCF genotype fields are
             //   lazy loaded, so they aren't caught elsewhere and made into User Exceptions
             exitSystemWithUserError(e);
+        } catch (net.sf.samtools.SAMException e) {
+            // Let's try this out and see how it is received by our users
+            exitSystemWithSamError(e);
         } catch (Exception e) {
             exitSystemWithError(e);
         }