fix for a numerical overflow error with the enumerate command

the issue was that for loci with more possible isoforms than can be
represented by an integer variable the count would overflow before
making the comparison with the user specified max_isoforms parameter.

To fix this I replaced the counter with a BigInteger, which won't
overflow.

IsoSCM/src/splicegraph/ExonSpliceGraph.java

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
+import java.math.BigInteger;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedList;
@@ -301,7 +302,7 @@ public static void iterateSpliceIsoforms(File assembly_gtf, GTFWriter isoform_gt
 
 		Set<String> skipped_ids = new HashSet<String>();
 		for(AnnotatedRegion r : exon_5p){	
-			if(max_paths == null || countPaths(r, exon_3p, sj5p) < max_paths){
+			if(max_paths == null || countPaths(r, exon_3p, sj5p).compareTo(new BigInteger(String.format("%d", max_paths))) < 0){
 				Stack<AnnotatedRegion> isoform_exons = new Stack<AnnotatedRegion>();
 				iterateIsoforms(isoform_count, isoform_exons, r, exon_3p, sj5p, isoform_gtf);
 			}
@@ -372,21 +373,22 @@ public static List<AnnotatedRegion> listChildren(AnnotatedRegion r, StrandedGeno
 		return children;
 	}
 
-	public static Integer countPaths(AnnotatedRegion r, StrandedGenomicIntervalTree<Map<String, Object>> exon_3p, StrandedGenomicIntervalTree<Map<String, Object>> sj5p){
+	public static BigInteger countPaths(AnnotatedRegion r, StrandedGenomicIntervalTree<Map<String, Object>> exon_3p, StrandedGenomicIntervalTree<Map<String, Object>> sj5p){
 		String path_att = "nPaths";
 
-		Integer nPaths = (Integer) r.getAttribute(path_att);
+		BigInteger nPaths = (BigInteger) r.getAttribute(path_att);
 
 		if(nPaths==null){
 			List<AnnotatedRegion> children = listChildren(r, exon_3p, sj5p);
 
 			if(children.size()==0){
-				nPaths=1;
+				nPaths=new BigInteger("1");
 			}
 			else{
-				nPaths = 0;
+				nPaths = new BigInteger("0");
 				for(AnnotatedRegion c : children){
-					nPaths += countPaths(c, exon_3p, sj5p);
+					nPaths = nPaths.add(countPaths(c, exon_3p, sj5p));
+//					nPaths += countPaths(c, exon_3p, sj5p);
 				}
 			}
 
@@ -420,7 +422,7 @@ public static void countSpliceIsoforms(File assembly_gtf) throws FileNotFoundExc
 		}
 
 		for(AnnotatedRegion r : exon_5p){	
-			int n = countPaths(r,exon_3p,sj5p);
+			int n = countPaths(r,exon_3p,sj5p).intValue();
 			System.out.printf("e5p %s %d\n", r,n);
 		}
 	}