Allowed > 2^31 hits

[rsem.git] / getUnique.cpp

diff --git a/getUnique.cpp b/getUnique.cpp
index 7272a810ca528f330a8b3ddb6efa12c090746b4e..c7925f2ca2a5a40694650088393eed77bd6f2c1c 100644 (file)
--- a/getUnique.cpp
+++ b/getUnique.cpp
@@ -9,6 +9,8 @@
 #include "sam/bam.h"
 #include "sam/sam.h"
 
+#include "utils.h"
+
 using namespace std;
 
 string cqname;
@@ -21,7 +23,7 @@ void output() {
        if (unaligned || arr.size() == 0) return;
        bool isPaired = (arr[0]->core.flag & 0x0001);
        if ((isPaired && arr.size() != 2) || (!isPaired && arr.size() != 1)) return;
-       for (int i = 0; i < (int)arr.size(); i++) samwrite(out, arr[i]);
+       for (size_t i = 0; i < arr.size(); i++) samwrite(out, arr[i]);
 }
 
 int main(int argc, char* argv[]) {
@@ -35,7 +37,7 @@ int main(int argc, char* argv[]) {
        out = samopen(argv[2], "wb", in->header);
        assert(out != 0);
 
-       int cnt = 0;
+       HIT_INT_TYPE cnt = 0;
 
        cqname = "";
        arr.clear();
@@ -46,7 +48,7 @@ int main(int argc, char* argv[]) {
                if (cqname != bam1_qname(b)) {
                        output();
                        cqname = bam1_qname(b);
-                       for (int i = 0; i < (int)arr.size(); i++) bam_destroy1(arr[i]);
+                       for (size_t i = 0; i < arr.size(); i++) bam_destroy1(arr[i]);
                        arr.clear();
                        unaligned = false;
                }