* mpileup *
***********/
+#define MPLP_VCF 0x1
+#define MPLP_VAR 0x2
+#define MPLP_AFS 0x4
+#define MPLP_AFALL 0x8
+
+#define MPLP_AFS_BLOCK 0x10000
+
typedef struct {
- int vcf, max_mq, min_mq;
+ int max_mq, min_mq, prior_type, flag;
+ double theta;
char *reg, *fn_pos;
faidx_t *fai;
kh_64_t *hash;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
+ uint64_t N = 0;
char *ref;
khash_t(64) *hash = 0;
// allocate
}
if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
// write the VCF header
- if (conf->vcf) {
+ if (conf->flag & MPLP_VCF) {
kstring_t s;
s.l = s.m = 0; s.s = 0;
+ puts("##fileformat=VCFv4.0");
+ puts("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">");
+ puts("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Non-reference allele frequency \\argmax_f P(D|f)\">");
+ puts("##INFO=<ID=AFE,Number=1,Type=Float,Description=\"Expected non-reference allele frequency\">");
+ puts("##FILTER=<ID=Q13,Description=\"All min{baseQ,mapQ} below 13\">");
kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
for (i = 0; i < n; ++i) {
const char *p;
free(s.s);
}
// mpileup
- if (conf->vcf) ma = mc_init(n);
+ if (conf->flag & MPLP_VCF) {
+ ma = mc_init(n);
+ mc_init_prior(ma, conf->prior_type, conf->theta);
+ }
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
ref_tid = tid;
}
- if (conf->vcf) {
- double f0, f; // the reference allele frequency
- int j, _ref, _alt, _ref0, depth, rms_q, _ref0b;
+ if (conf->flag & MPLP_VCF) {
+ mc_rst_t r;
+ int j, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0, level = 2, tot;
uint64_t sqr_sum;
+ if (conf->flag & MPLP_AFS) level = 3;
_ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
_ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
- f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
- if (f >= 0.0) {
- double flast = f;
- for (j = 0; j < 10; ++j) {
- f = mc_freq_iter(flast, ma);
- if (fabs(f - flast) < 1e-3) break;
- flast = f;
- }
+ tot = mc_cal(_ref0, n_plp, plp, ma, &r, level);
+ if (tot) { // has good bases
+ double q;
+ is_var = (r.p_ref < .5);
+ q = is_var? r.p_ref : 1. - r.p_ref;
+ if (q < 1e-308) q = 1e-308;
+ qref = (int)(-3.434 * log(q) + .499);
+ if (qref > 99) qref = 99;
}
+ if ((conf->flag & MPLP_VAR) && !is_var) continue;
+ ++N; // number of processed lines
printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
- if (_ref0 == _ref) putchar("ACGTN"[_alt]);
- else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
- printf("\t0\t"); // FIXME: currently these not available
- if (f0 < 0.) printf("Q13\t");
+ if (is_var) {
+ putchar("ACGTN"[r.alt]);
+ if (r.alt2 >= 0 && r.alt2 < 4) printf(",%c", "ACGT"[r.alt2]);
+ } else putchar('.');
+ printf("\t%d\t", qref);
+ if (!tot) printf("Q13\t");
else printf(".\t");
for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
depth += n_plp[i];
}
}
rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
- printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f);
- printf("\tDP");
- // output genotype information; FIXME: to be implmented...
- for (i = 0; i < n; ++i)
- printf("\t%d", n_plp[i]);
+ printf("DP=%d;MQ=%d", depth, rms_q);
+ if (tot) {
+ printf(";AF=%.3lf", 1. - r.f_em);
+ if (level >= 2) printf(";AFE=%.3lf", 1-r.f_exp);
+ if (conf->flag & MPLP_AFALL) {
+ printf(";AF0=%.3lf;AFN=%.3lf", 1-r.f_naive, 1-r.f_nielsen);
+ if (conf->flag & MPLP_AFS) printf(";AFB=%.3lf", 1-r.f_map);
+ }
+ }
+ printf("\tGT:GQ:DP");
+ if (tot) {
+ for (i = 0; i < n; ++i) {
+ int x = mc_call_gt(ma, r.f_exp, i);
+ printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
+ }
+ } else for (i = 0; i < n; ++i) printf("\t./.:0:0");
putchar('\n');
+ if (N % MPLP_AFS_BLOCK == 0) mc_dump_afs(ma);
} else {
printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
putchar('\n');
}
}
+ if ((conf->flag&MPLP_VCF) && (conf->flag&MPLP_AFS)) mc_dump_afs(ma);
if (hash) { // free the hash table
khint_t k;
for (k = kh_begin(hash); k < kh_end(hash); ++k)
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
- while ((c = getopt(argc, argv, "f:r:l:VM:q:")) >= 0) {
+ mplp.prior_type = MC_PTYPE_FULL;
+ mplp.theta = 1e-3;
+ while ((c = getopt(argc, argv, "vVcFSP:f:r:l:VM:q:t:")) >= 0) {
switch (c) {
+ case 't': mplp.theta = atof(optarg); break;
+ case 'P':
+ if (strcmp(optarg, "full") == 0) mplp.prior_type = MC_PTYPE_FULL;
+ else if (strcmp(optarg, "cond2") == 0) mplp.prior_type = MC_PTYPE_COND2;
+ else if (strcmp(optarg, "flat") == 0) mplp.prior_type = MC_PTYPE_FLAT;
+ else {
+ fprintf(stderr, "[%s] unrecognized prior type.\n", __func__);
+ return 1;
+ }
+ break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); break;
- case 'V': mplp.vcf = 1; break;
+ case 'V':
+ case 'c': mplp.flag |= MPLP_VCF; break;
+ case 'S': mplp.flag |= MPLP_AFS; break;
+ case 'F': mplp.flag |= MPLP_AFALL; break;
+ case 'v': mplp.flag |= MPLP_VAR; break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
}
}
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, " -t FLOAT scaled mutation rate [%lg]\n", mplp.theta);
+ fprintf(stderr, " -P STR prior: full, flat, cond2 [full]\n");
+ fprintf(stderr, " -c generate VCF output (consensus calling)\n");
+ fprintf(stderr, " -v show variant sites only\n");
+ fprintf(stderr, " -S calculate AFS (slow, to stderr)\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
return 1;
}
mpileup(&mplp, argc - optind, argv + optind);
projects / samtools.git / blobdiff