diff --git a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
index a3f0a0444..2a3999032 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
@@ -118,21 +118,30 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
     }
 
     public ReferenceSequence getSequence( String contig ) {
-        return getSubsequenceAt( contig, 0, (int)index.getIndexEntry(contig).getSize() );
+        return getSubsequenceAt( contig, 0, (int)index.getIndexEntry(contig).getSize()-1 );
     }
 
-    public ReferenceSequence getSubsequenceAt( String contig, int pos, int length ) {
+    public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
+        if(start > stop)
+            throw new PicardException(String.format("Malformed query; start point %d lies after end point %d",start,stop));
+        if(start > Integer.MAX_VALUE)
+            throw new PicardException("Due to current ReferenceSequence limitations, a start point larger than Integer.MAX_VALUE cannot be loaded.");
+        if(stop - start + 1 > Integer.MAX_VALUE)
+            throw new PicardException("Due to current ReferenceSequence limitations, a region larger than Integer.MAX_VALUE cannot be loaded.");
+
         FastaSequenceIndexEntry indexEntry = index.getIndexEntry(contig);
 
-        if(pos + length - 1 > indexEntry.getSize())
+        if(stop > indexEntry.getSize())
             throw new PicardException("Query asks for data past end of contig");
 
+        int length = (int)(stop - start + 1);
+
         final int basesPerLine = indexEntry.getBasesPerLine();
         final int bytesPerLine = indexEntry.getBytesPerLine();
 
         // Start reading at the closest start-of-line to our data.
-        long readStart = indexEntry.getLocation() + (pos / basesPerLine) * bytesPerLine;
-        int dataOfInterestStart = pos % basesPerLine;
+        long readStart = indexEntry.getLocation() + (start / basesPerLine) * bytesPerLine;
+        int dataOfInterestStart = (int)(start % basesPerLine);
 
         byte[] accumulator = new byte[length];
         int nextAccumulatorSlot = 0;        
@@ -158,7 +167,7 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
             dataOfInterestStart = 0;
         }
 
-        return new ReferenceSequence( contig, pos, accumulator );
+        return new ReferenceSequence( contig, (int)start, accumulator );
     }
 
     /**
diff --git a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java b/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
index 8a0719402..300d8eb99 100755
--- a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
+++ b/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
@@ -53,7 +53,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
     @Test
     public void testFirstSequence() {
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,firstBasesOfChrM.length());
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,firstBasesOfChrM.length()-1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM");
@@ -67,7 +67,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
     @Test
     public void testFirstSequenceExtended() {
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,extendedBasesOfChrM.length());
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",0,extendedBasesOfChrM.length()-1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM");
@@ -84,7 +84,9 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
         String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
 
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM", bytesToChopOff ,truncated.length() );
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
+                                                                   bytesToChopOff,
+                                                                   bytesToChopOff + truncated.length() - 1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM");
@@ -101,7 +103,9 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
         String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
 
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM", bytesToChopOff, truncated.length() );
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
+                                                                   bytesToChopOff,
+                                                                   bytesToChopOff + truncated.length() - 1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM");
@@ -133,7 +137,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
     public void testReadThroughEndOfContig() {
         long startTime = System.currentTimeMillis();
         try {
-            ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16500,100);
+            ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16500,16600);
         }
         finally {
             long endTime = System.currentTimeMillis();
@@ -145,7 +149,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
      public void testReadPastEndOfContig() {
          long startTime = System.currentTimeMillis();
          try {
-             ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16800,100);
+             ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16800,16900);
          }
          finally {
              long endTime = System.currentTimeMillis();
@@ -193,7 +197,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
     @Test
     public void testFirstOfChr1() {
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",0,firstBasesOfChr1.length());
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",0,firstBasesOfChr1.length()-1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr1");
@@ -207,7 +211,7 @@ public class IndexedFastaSequenceFileTest extends BaseTest {
     @Test
     public void testFirstOfChr8() {
         long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",0,firstBasesOfChr8.length());
+        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",0,firstBasesOfChr8.length()-1);
         long endTime = System.currentTimeMillis();
 
         Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr8");