#include <cstring>
#include <cstdlib>
#include <cassert>
+#include <iostream>
#include <stdint.h>
#include "sam/bam.h"
#include "sam/sam.h"
+#include "utils.h"
#include "wiggle.h"
void add_bam_record_to_wiggle(const bam1_t *b, Wiggle& wiggle) {
memset(used, 0, sizeof(bool) * header->n_targets);
int cur_tid = -1; //current tid;
- int cnt = 0;
+ HIT_INT_TYPE cnt;
bam1_t *b = bam_init1();
Wiggle wiggle;
while (samread(bam_in, b) >= 0) {
}
add_bam_record_to_wiggle(b, wiggle);
++cnt;
- if (cnt % 1000000 == 0) fprintf(stderr, "%d FIN\n", cnt);
+ if (cnt % 1000000 == 0) std::cout<< cnt<< std::endl;
}
if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }