From e1d69e4060b4791f126eaf534f12152c5e067b98 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 1 Feb 2012 19:34:39 -0500
Subject: [PATCH] make the size of a GenomeLoc int instead of long

it will never be bigger than an int and it's actually useful to be an int so we can use it as parameters to array/list/hash size creation.
---
 .../src/org/broadinstitute/sting/utils/GenomeLoc.java    | 2 +-
 .../sting/utils/interval/IntervalUtils.java              | 4 ++--
 .../sting/utils/interval/IntervalUtilsUnitTest.java      | 9 ++++-----
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index ad10b61e7..41ca58157 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -436,7 +436,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
      *         never be < 1.
      */
     @Ensures("result > 0")
-    public long size() {
+    public int size() {
         return stop - start + 1;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index f8655f74a..ea1eaeb51 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -314,10 +314,10 @@ public class IntervalUtils {
      * @param reference The reference for the intervals.
      * @return A map of contig names with their sizes.
      */
-    public static Map<String, Long> getContigSizes(File reference) {
+    public static Map<String, Integer> getContigSizes(File reference) {
         ReferenceDataSource referenceSource = new ReferenceDataSource(reference);
         List<GenomeLoc> locs = GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference().getSequenceDictionary()).toList();
-        Map<String, Long> lengths = new LinkedHashMap<String, Long>();
+        Map<String, Integer> lengths = new LinkedHashMap<String, Integer>();
         for (GenomeLoc loc: locs)
             lengths.put(loc.getContig(), loc.size());
         return lengths;
diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
index a9035ffd9..0a8caa8cc 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
@@ -8,13 +8,12 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.IntervalBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.testng.Assert;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -341,7 +340,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @Test
     public void testGetContigLengths() {
-        Map<String, Long> lengths = IntervalUtils.getContigSizes(new File(BaseTest.hg18Reference));
+        Map<String, Integer> lengths = IntervalUtils.getContigSizes(new File(BaseTest.hg18Reference));
         Assert.assertEquals((long)lengths.get("chr1"), 247249719);
         Assert.assertEquals((long)lengths.get("chr2"), 242951149);
         Assert.assertEquals((long)lengths.get("chr3"), 199501827);