Release 0.12.7 bugfix for division by zero bug

apeltzer · Dec 23, 2020 · 07d4786 · 07d4786
1 parent 5abdc65
commit 07d4786
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,5 +1,5 @@
 group 'com.uni-tuebingen.de.it.eager.dedup'
-version '0.12.7'
+version '0.12.8'
 
 apply plugin: 'java'
 apply plugin: 'idea'

diff --git a/src/main/java/RMDupper.java b/src/main/java/RMDupper.java
@@ -52,7 +52,7 @@
  */
 public class RMDupper{
     private static final String CLASS_NAME = "dedup";
-    private static final String VERSION = "0.12.7";
+    private static final String VERSION = "0.12.8";
     private static boolean piped = true;
 
     private final Boolean allReadsAsMerged;
@@ -273,8 +273,13 @@ public static void main(String[] args) throws IOException {
                 metric_map.put("forward_removed", rmdup.dupStats.removed_forward);
                 metric_map.put("merged_removed", rmdup.dupStats.removed_merged);
                 metric_map.put("total_removed", rmdup.dupStats.removed_forward + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_merged);
-                metric_map.put("dup_rate", df.format((double) (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.mapped_reads));
-                metric_map.put("clusterfactor", df.format( (1.0 + (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.mapped_reads)));
+                if(rmdup.dupStats.mapped_reads == 0 ) { //Division by zero bugfix for low coverage / no mapped reads case
+                    metric_map.put("dup_rate", df.format((double) 0));
+                    metric_map.put("clusterfactor", df.format((double) 0));
+                } else {
+                    metric_map.put("dup_rate", df.format((double) (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.mapped_reads));
+                    metric_map.put("clusterfactor", df.format( (1.0 + (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.mapped_reads)));
+                }
 
                 json_map.put("metrics", metric_map);
                 Gson gson = new GsonBuilder().setPrettyPrinting().create();