--- /dev/null
+#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;
+}