#include<cassert>
#include<string>
#include<sstream>
+#include<iostream>
#include <stdint.h>
#include "sam/bam.h"
#include "sam_rsem_aux.h"
#include "sam_rsem_cvt.h"
+#include "utils.h"
+
#include "SingleHit.h"
#include "PairedEndHit.h"
bam1_t *b;
SingleHit *hit;
- int cnt = 0;
+ HIT_INT_TYPE cnt = 0;
b = bam_init1();
while (samread(in, b) >= 0) {
++cnt;
- if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
+ if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
if (b->core.flag & 0x0004) continue;
assert(wrapper.getNextHit() == NULL);
bam_destroy1(b);
- if (verbose) { printf("Bam output file is generated!\n"); }
+ if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
}
void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
cnt += 2;
- if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
-
+ if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
//mate info is not complete, skip
if (!(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)))) continue;
//unalignable reads, skip
bam_destroy1(b);
bam_destroy1(b2);
- if (verbose) { printf("Bam output file is generated!\n"); }
+ if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
}
void BamWriter::convert(bam1_t *b, double prb) {