#include "sam/bam.h"
#include "sam/sam.h"
+#include "utils.h"
+
using namespace std;
string cqname;
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]);
+ if ((isPaired && arr.size() != 2) || (!isPaired && arr.size() != 1)) return;
+ for (size_t i = 0; i < arr.size(); i++) samwrite(out, arr[i]);
}
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();
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;
}