f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
if (f >= 0.0) {
double q, flast = f;
- for (j = 0; j < 10; ++j){
+ for (j = 0; j < 10; ++j) {
f = mc_freq_iter(flast, ma);
+// printf("%lg->%lg\n", flast, f);
if (fabs(f - flast) < 1e-3) break;
flast = f;
}
+ if (1. - f < 1e-4) f = 1.;
pref = mc_ref_prob(ma);
is_var = (pref < .5);
q = is_var? pref : 1. - pref;
}
}
if (argc == 1) {
- fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+ fprintf(stderr, "Options: -f FILE reference sequence file [null]\n");
+ fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n");
+ fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
+ fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(stderr, " -V generate VCF output (SNP calling)\n");
+ fprintf(stderr, " -v show variant sites only\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
return 1;
}
mpileup(&mplp, argc - optind, argv + optind);