Description: Catch the IOException launched by close() method of LineIterator
Author: Pierre Gruet <pgt@debian.org>
Forwarded: https://github.com/CampagneLaboratory/goby3/issues/7
Last-Update: 2020-11-03

--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/EmpiricalPMode.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/EmpiricalPMode.java
@@ -342,7 +342,12 @@
             Object next = it.next();
             lineCount++;
         }
-        it.close();
+        try {
+            it.close();
+        } catch (IOException e) {
+            System.err.println("Could not close LineIterator on " + inputFilename);
+            System.exit(1);
+        }
         return lineCount;
     }