bam_flagstat_t *s;
bam1_t *b;
bam1_core_t *c;
+ int ret;
s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
b = bam_init1();
c = &b->core;
- while (bam_read1(fp, b) >= 0) {
+ while ((ret = bam_read1(fp, b)) >= 0)
flagstat_loop(s, c);
- }
bam_destroy1(b);
+ if (ret != -1)
+ fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
return s;
}
int bam_flagstat(int argc, char *argv[])