X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=blobdiff_plain;f=src%2Fapi%2Finternal%2Findex%2FBamStandardIndex_p.cpp;h=2606a98db53b74fab3b3cadae0a765e033ccd75a;hp=dcdec8d2ab753b749522774a98eb1b41e7eb883b;hb=6111130f6d7b1ae06ac25178f8dc5006f0754cfc;hpb=6708a21b48a6021b10a544ef4fecef5f1aa0dd1d

diff --git a/src/api/internal/index/BamStandardIndex_p.cpp b/src/api/internal/index/BamStandardIndex_p.cpp
index dcdec8d..2606a98 100644
--- a/src/api/internal/index/BamStandardIndex_p.cpp
+++ b/src/api/internal/index/BamStandardIndex_p.cpp
@@ -2,7 +2,7 @@
 // BamStandardIndex.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 10 November 2011 (DB)
+// Last modified: 25 May 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides index operations for the standardized BAM index format (".bai")
 // ***************************************************************************
@@ -389,17 +389,17 @@ bool BamStandardIndex::Create(void) {
         }
 
         // after finishing alignments, if any data was read, check:
-        if ( currentRefID >= 0 ) {
+        if ( lastOffset != currentOffset ) {
 
             // store last alignment chunk to its bin, then write last reference entry with data
             SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset);
             WriteReferenceEntry(refEntry);
+        }
 
-            // then write any empty references remaining at end of file
-            for ( int i = currentRefID+1; i < numReferences; ++i ) {
-                BaiReferenceEntry emptyEntry(i);
-                WriteReferenceEntry(emptyEntry);
-            }
+        // then write any empty references remaining at end of file
+        for ( int i = currentRefID+1; i < numReferences; ++i ) {
+            BaiReferenceEntry emptyEntry(i);
+            WriteReferenceEntry(emptyEntry);
         }
 
     } catch ( BamException& e) {