From cd711d7697ed5ce3a54be23fd5036414ec453c85 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 21 Aug 2009 05:35:49 +0000
Subject: [PATCH] Added detection of interval files with zero length to the
 GATK, and removed it from the interval merger walker: this was a critical
 blocking emergency issue for Eric.

also fixed some verbage in the GAEngine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1449 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/GenomeAnalysisEngine.java  | 4 ++--
 .../sting/gatk/walkers/indels/IntervalMergerWalker.java  | 9 ---------
 .../org/broadinstitute/sting/utils/GenomeLocParser.java  | 8 ++++++--
 3 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 3f41e9bbb..26aaefc1d 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -103,12 +103,12 @@ public class GenomeAnalysisEngine {
     public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
         // validate our parameters
         if (args == null) {
-            throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can be null.");
+            throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
         }
 
         // validate our parameters
         if (my_walker == null)
-            throw new StingException("The walker passed to GenomeAnalysisEngine can be null.");
+            throw new StingException("The walker passed to GenomeAnalysisEngine can not be null.");
 
         // save our argument parameter
         this.argCollection = args;
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 8e9c209f0..d4e39d390 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -114,15 +114,6 @@ 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 )
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 481928169..fe5ac3b94 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -321,8 +321,12 @@ public class GenomeLocParser {
          */
         List<GenomeLoc> ret = null;
         try {
-            IntervalList il = IntervalList.fromFile(new File(file_name));
-
+            File inputFile = new File(file_name);
+            
+            // sometimes we see an empty file passed as a parameter, if so return an empty list
+            if (inputFile.length() < 1) return new ArrayList<GenomeLoc>();
+            IntervalList il = IntervalList.fromFile(inputFile);
+            
             // iterate through the list of merged intervals and add then as GenomeLocs
             ret = new ArrayList<GenomeLoc>();
             for (Interval interval : il.getUniqueIntervals()) {