X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=TabixReader.java;h=5874202581ee8bf72f4b0c3917a743f59c40c03e;hp=40d395120e4df26cbf04a7667fba2775a921a05b;hb=3be5ff47495762af7f2ebec145bc8f9c7674593d;hpb=f14cecb6523bd4275c2858c2d54167c94db25ede

diff --git a/TabixReader.java b/TabixReader.java
index 40d3951..5874202 100644
--- a/TabixReader.java
+++ b/TabixReader.java
@@ -217,7 +217,7 @@ public class TabixReader
 		int[] ret = new int[3];
 		colon = reg.indexOf(':'); hyphen = reg.indexOf('-');
 		chr = colon >= 0? reg.substring(0, colon) : reg;
-		ret[1] = colon >= 0? Integer.parseInt(reg.substring(colon+1, hyphen)) - 1 : 0;
+		ret[1] = colon >= 0? Integer.parseInt(reg.substring(colon+1, hyphen >= 0? hyphen : reg.length())) - 1 : 0;
 		ret[2] = hyphen >= 0? Integer.parseInt(reg.substring(hyphen+1)) : 0x7fffffff;
 		ret[0] = chr2tid(chr);
 		return ret;
@@ -339,6 +339,7 @@ public class TabixReader
 				for (int j = 0; j < chunks.length; ++j)
 					if (less64(min_off, chunks[j].v))
 						off[n_off++] = new TPair64(chunks[j]);
+		if (n_off == 0) return null;
 		Arrays.sort(off, 0, n_off);
 		// resolve completely contained adjacent blocks
 		for (i = 1, l = 0; i < n_off; ++i) {
@@ -385,7 +386,7 @@ public class TabixReader
 					System.out.println(s);
 			} else { // a region is specified; random access
 				TabixReader.Iterator iter = tr.query(args[1]); // get the iterator
-				while ((s = iter.next()) != null)
+				while (iter != null && (s = iter.next()) != null)
 					System.out.println(s);
 			}
 		} catch (IOException e) {