#include "bam.h"
typedef struct {
- long long n_reads, n_mapped, n_pair_all, n_pair_map, n_pair_good;
- long long n_sgltn, n_read1, n_read2;
- long long n_qcfail, n_dup;
- long long n_diffchr, n_diffhigh;
+ long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+ long long n_sgltn[2], n_read1[2], n_read2[2];
+ long long n_dup[2];
+ long long n_diffchr[2], n_diffhigh[2];
} bam_flagstat_t;
#define flagstat_loop(s, c) do { \
- ++(s)->n_reads; \
+ int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \
+ ++(s)->n_reads[w]; \
if ((c)->flag & BAM_FPAIRED) { \
- ++(s)->n_pair_all; \
- 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; \
+ ++(s)->n_pair_all[w]; \
+ if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w]; \
+ if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w]; \
+ if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w]; \
+ if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w]; \
if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
- ++(s)->n_pair_map; \
+ ++(s)->n_pair_map[w]; \
if ((c)->mtid != (c)->tid) { \
- ++(s)->n_diffchr; \
- if ((c)->qual >= 5) ++(s)->n_diffhigh; \
+ ++(s)->n_diffchr[w]; \
+ if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \
} \
} \
} \
- if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped; \
- if ((c)->flag & BAM_FQCFAIL) ++(s)->n_qcfail; \
- if ((c)->flag & BAM_FDUP) ++(s)->n_dup; \
+ if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w]; \
+ if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w]; \
} while (0)
bam_flagstat_t *bam_flagstat_core(bamFile fp)
assert(fp);
header = bam_header_read(fp);
s = bam_flagstat_core(fp);
- 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 (%.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 (%.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);
+ printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+ printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+ printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0);
+ printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+ printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+ printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+ printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+ printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+ printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
free(s);
bam_header_destroy(header);
bam_close(fp);
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