Fixed: regression in convert tool - SAM tags contained unreadable chars for int8...

[bamtools.git] / src / toolkit / bamtools_count.cpp

diff --git a/src/toolkit/bamtools_count.cpp b/src/toolkit/bamtools_count.cpp
index 3c46f679d93c2e2860af15b3439cbb5d7ec936c3..3593f4d448536b9894910232a7894d57fcb42205 100644 (file)
--- a/src/toolkit/bamtools_count.cpp
+++ b/src/toolkit/bamtools_count.cpp
@@ -9,6 +9,7 @@
 
 #include "bamtools_count.h"
 
+#include <api/BamAlgorithms.h>
 #include <api/BamMultiReader.h>
 #include <utils/bamtools_options.h>
 #include <utils/bamtools_utilities.h>
@@ -95,7 +96,7 @@ bool CountTool::CountToolPrivate::Run(void) {
             reader.LocateIndexes();
 
             // if index data available for all BAM files, we can use SetRegion
-            if ( reader.IsIndexLoaded() ) {
+            if ( reader.HasIndexes() ) {
 
                 // attempt to set region on reader
                 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {