bugfix

jodyphelan · Oct 17, 2024 · 7d5ca01 · 7d5ca01
1 parent 7d8bc7e
commit 7d5ca01
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/pathogenprofiler/bam.py b/pathogenprofiler/bam.py
@@ -356,7 +356,10 @@ def calculate_bamstats(self):
             if row[0]!="SN": continue
             if row[1]=='raw total sequences:': self.total_reads = int(row[2])
             if row[1]=='reads mapped:': self.mapped_reads = int(row[2])
-        self.pct_reads_mapped = round(self.mapped_reads/self.total_reads*100,2)
+        if self.total_reads==0:
+            self.pct_reads_mapped = 0
+        else:
+            self.pct_reads_mapped = round(self.mapped_reads/self.total_reads*100,2)
         os.remove(temp_file)
 
     def get_missing_genomic_positions(self, bed_file:str, cutoff: int=10) -> List[GenomePositionDepth]: