From ad60300bee61f97c26a5e6f186b21093643b5e57 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 12 Oct 2012 09:07:57 -0400
Subject: [PATCH] Catch malformed BAM files at the source since this is the
 largest class of errors in Tableau.

---
 .../sting/gatk/datasources/reads/SAMDataSource.java         | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index 8562ace98..bb788c89f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -1008,6 +1008,12 @@ public class SAMDataSource {
             } catch ( SAMFormatException e ) {
                 throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
             }
+            // Picard is throwing a RuntimeException here when BAMs are malformed with bad headers (and so look like SAM files).
+            // Let's keep this separate from the SAMFormatException (which ultimately derives from RuntimeException) case,
+            // just in case we want to change this behavior later.
+            catch ( RuntimeException e ) {
+                throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
+            }
             reader.setSAMRecordFactory(factory);
             reader.enableFileSource(true);
             reader.setValidationStringency(validationStringency);