Allowed > 2^31 hits

[rsem.git] / scanForPairedEndReads.cpp

diff --git a/scanForPairedEndReads.cpp b/scanForPairedEndReads.cpp
index 4d1fbfb79ea16d52a0e1b903bd0e40cfc11f66cd..751fa558833aabce8bac0ae4d02013aae0ac1685 100644 (file)
--- a/scanForPairedEndReads.cpp
+++ b/scanForPairedEndReads.cpp
@@ -10,6 +10,7 @@
 #include "sam/bam.h"
 #include "sam/sam.h"
 
+#include "utils.h"
 #include "my_assert.h"
 
 using namespace std;
@@ -55,7 +56,7 @@ int main(int argc, char* argv[]) {
        string qname;
        bool go_on = (samread(in, b) >= 0);
        bool isPaired;
-       long cnt = 0;
+       HIT_INT_TYPE cnt = 0;
 
        printf("."); fflush(stdout);