From 1e8b97b5604578f1c31ce7a3db75c8adbb99aa2b Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 17 Aug 2009 20:19:14 +0000
Subject: [PATCH] quietly skip empty intervals files rather than crash.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1428 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IntervalMergerWalker.java  | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index 9358162c2..8e9c209f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -33,6 +33,9 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
+import java.io.*;
+
+
 /**
  * Merges intervals based on reads which overlap them.
  */
@@ -111,6 +114,15 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
      * @return a linked list of sorted, merged intervals.
      */
     private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
+
+		// ignore zero-length intervals files.
+		for (int i = 0; i < intervalsSource.size(); i++) 
+		{
+			File f = new File(intervalsSource.get(i));
+			long size = f.length();
+			if (size == 0) { intervalsSource.remove(i); }
+		}
+
         List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
         GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet();
         for ( GenomeLoc parsedInterval : parsedIntervals )
@@ -118,4 +130,4 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 
         return new LinkedList<GenomeLoc>( intervalSortedSet );
     }
-}
\ No newline at end of file
+}