--- a/varscan_somatic.xml	Mon Jan 21 12:05:00 2019 -0500
+++ b/varscan_somatic.xml	Thu Mar 28 18:19:00 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.3">
+<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.4">
     <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
     <macros>
         <import>macros.xml</import>
@@ -453,6 +453,33 @@
                 <expand macro="test_mentions_filters" />
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <!-- Test with an input bam with extremely high coverage at a
+            variant site (high enough to trigger an AssertionError from
+            pysam.libcalignedsegment.get_query_sequences) to see if the
+            tool can handle this.
+            Also test that the tool doesn't report SNVs against Ns in
+            the reference genome (this would lead to more than one variant
+            getting called). -->
+            <conditional name="reference">
+                <param name="source" value="history" />
+                <param name="genome" value="hg19_chrM.fa" />
+            </conditional>
+            <param name="normal_bam" value="high_cov_chrM.bam" />
+            <param name="tumor_bam" value="high_cov_chrM.bam" />
+            <param name="split_output" value="false" />
+            <conditional name="call_params">
+                <param name="settings" value="varscan_defaults" />
+            </conditional>
+            <conditional name="filter_params">
+                <param name="settings" value="varscan_defaults" />
+            </conditional>
+            <output name="output">
+                <expand macro="test_mentions_contig" />
+                <expand macro="test_mentions_filters" />
+                <metadata name="data_lines" value="1" />
+            </output>
+        </test>
     </tests>
 
     <help>