+#include <unistd.h>
+#include <assert.h>
#include "bam.h"
typedef struct {
if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good; \
if ((c)->flag & BAM_FREAD1) ++(s)->n_read1; \
if ((c)->flag & BAM_FREAD2) ++(s)->n_read2; \
- if ((c)->flag & BAM_FMUNMAP) ++(s)->n_sgltn; \
+ if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn; \
if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
++(s)->n_pair_map; \
if ((c)->mtid != (c)->tid) { \
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[])
printf("%lld in total\n", s->n_reads);
printf("%lld QC failure\n", s->n_qcfail);
printf("%lld duplicates\n", s->n_dup);
- printf("%lld mapped\n", s->n_mapped);
+ printf("%lld mapped (%.2f%%)\n", s->n_mapped, (float)s->n_mapped / s->n_reads * 100.0);
printf("%lld paired in sequencing\n", s->n_pair_all);
printf("%lld read1\n", s->n_read1);
printf("%lld read2\n", s->n_read2);
- printf("%lld properly paired\n", s->n_pair_good);
- printf("%lld with both itself and its mate mapped\n", s->n_pair_map);
- printf("%lld singletons\n", s->n_sgltn);
- printf("%lld with its mate mapped to a different chr\n", s->n_diffchr);
+ printf("%lld properly paired (%.2f%%)\n", s->n_pair_good, (float)s->n_pair_good / s->n_pair_all * 100.0);
+ printf("%lld with itself and mate mapped\n", s->n_pair_map);
+ printf("%lld singletons (%.2f%%)\n", s->n_sgltn, (float)s->n_sgltn / s->n_pair_all * 100.0);
+ printf("%lld with mate mapped to a different chr\n", s->n_diffchr);
+ printf("%lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh);
free(s);
bam_header_destroy(header);
bam_close(fp);