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#include "pysam.h"
#include <unistd.h>
#include <assert.h>
#include "bam.h"
typedef struct {
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 { \
int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \
++(s)->n_reads[w]; \
if ((c)->flag & BAM_FPAIRED) { \
++(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[w]; \
if ((c)->mtid != (c)->tid) { \
++(s)->n_diffchr[w]; \
if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \
} \
} \
} \
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)
{
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 ((ret = bam_read1(fp, b)) >= 0)
flagstat_loop(s, c);
bam_destroy1(b);
if (ret != -1)
fprintf(pysamerr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
return s;
}
int bam_flagstat(int argc, char *argv[])
{
bamFile fp;
bam_header_t *header;
bam_flagstat_t *s;
if (argc == optind) {
fprintf(pysamerr, "Usage: samtools flagstat <in.bam>\n");
return 1;
}
fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
assert(fp);
header = bam_header_read(fp);
s = bam_flagstat_core(fp);
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);
return 0;
}
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