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;
}
int bam_flagstat(int argc, char *argv[])
{
samFile *fp;
bam_hdr_t *header;
bam_flagstat_t *s;
char b0[16], b1[16];
int c;
enum {
INPUT_FMT_OPTION = CHAR_MAX+1,
};
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '@'),
{NULL, 0, NULL, 0}
};
while ((c = getopt_long(argc, argv, "@:", lopts, NULL)) >= 0) {
switch (c) {
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
/* else fall-through */
case '?':
usage_exit(samtools_stderr, EXIT_FAILURE);
}
}
if (argc != optind+1) {
if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS);
else usage_exit(samtools_stderr, EXIT_FAILURE);
}
fp = sam_open_format(argv[optind], "r", &ga.in);
if (fp == NULL) {
print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]);
return 1;
}
if (ga.nthreads > 0)
hts_set_threads(fp, ga.nthreads);
if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS,
SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) {
fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
return 1;
}
if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) {
fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
return 1;
}
header = sam_hdr_read(fp);
if (header == NULL) {
fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]);
return 1;
}
s = bam_flagstat_core(fp, header);
fprintf(samtools_stdout, "%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
fprintf(samtools_stdout, "%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]);
fprintf(samtools_stdout, "%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]);
fprintf(samtools_stdout, "%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
fprintf(samtools_stdout, "%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
fprintf(samtools_stdout, "%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
fprintf(samtools_stdout, "%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
fprintf(samtools_stdout, "%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
fprintf(samtools_stdout, "%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
fprintf(samtools_stdout, "%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
fprintf(samtools_stdout, "%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
free(s);
bam_hdr_destroy(header);
sam_close(fp);
sam_global_args_free(&ga);
return 0;
}