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

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;

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 )

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -321,7 +321,11 @@ 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>();