From c312bd59600c941afc99b7708e156765d62ce3be Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Tue, 24 Jan 2012 15:30:04 -0500
Subject: [PATCH] Weirdly, PicardException inherits from SAMException, which
 means that our specialty code for reporting malformed BAMs was actually
 misreporting any error that happened in the Picard layer as a BAM ERROR.

Specifically changing PicardException to report as a ReviewedStingException; we might want to
change it in the future.  I'll followup with the Picard team to make sure they really, really
want PicardException to inherit from SAMException.
---
 .../org/broadinstitute/sting/gatk/CommandLineGATK.java    | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index b4d337d8d..9c59ffe9a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk;
 
+import net.sf.picard.PicardException;
+import net.sf.samtools.SAMException;
 import org.broad.tribble.TribbleException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
@@ -95,7 +97,11 @@ 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) {
+        } catch(PicardException e) {
+            // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions?
+            exitSystemWithError(e);
+        }
+        catch (SAMException e) {
             checkForTooManyOpenFilesProblem(e.getMessage());
             exitSystemWithSamError(e);
         } catch (Throwable t) {