#include "faidx.h"
#include "bam_maqcns.h"
#include "bam_mcns.h"
+#include "bam2bcf.h"
#include "khash.h"
#include "glf.h"
#include "kstring.h"
* mpileup *
***********/
+#define MPLP_VCF 0x1
+#define MPLP_VAR 0x2
+#define MPLP_AFALL 0x8
+#define MPLP_GLF 0x10
+#define MPLP_NO_COMP 0x20
+
+#define MPLP_AFS_BLOCK 0x10000
+
typedef struct {
- int vcf, max_mq, min_mq, var_only, prior_type;
+ int max_mq, min_mq, prior_type, flag, min_baseQ;
double theta;
char *reg, *fn_pos;
faidx_t *fai;
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
mplp_aux_t **data;
- mc_aux_t *ma = 0;
int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
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
+
+ mc_aux_t *ma = 0;
+
+ bcf_callaux_t *bca = 0;
+ bcf_callret1_t *bcr = 0;
+ bcf_call_t bc;
+ bcf_t *bp = 0;
+
+ memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(void*));
plp = calloc(n, sizeof(void*));
n_plp = calloc(n, sizeof(int*));
+
// read the header and initialize data
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
}
if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
// write the VCF header
- if (conf->vcf) {
+ if (conf->flag & MPLP_GLF) {
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
+ for (i = 0; i < h->n_targets; ++i) {
+ kputs(h->target_name[i], &s);
+ kputc('\0', &s);
+ }
+ bp->h.l_nm = s.l;
+ bp->h.name = malloc(s.l);
+ memcpy(bp->h.name, s.s, s.l);
+ s.l = 0;
+ for (i = 0; i < n; ++i) {
+ const char *p;
+ if ((p = strstr(fn[i], ".bam")) != 0)
+ kputsn(fn[i], p - fn[i], &s);
+ else kputs(fn[i], &s);
+ kputc('\0', &s);
+ }
+ bp->h.l_smpl = s.l;
+ bp->h.sname = malloc(s.l);
+ memcpy(bp->h.sname, s.s, s.l);
+ bp->h.l_txt = 0;
+ free(s.s);
+ bcf_hdr_sync(&bp->h);
+ bcf_hdr_write(bp);
+ } else 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=\"Posterior non-reference allele frequency\">");
- puts("##INFO=<ID=AFEM,Number=1,Type=Float,Description=\"Prior-free non-reference allele frequency by EM\">");
+ 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\">");
+ puts("##FILTER=<ID=FPE,Description=\"Floating point error\">");
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) {
+ if (conf->flag & MPLP_GLF) {
+ bca = bcf_call_init(-1., conf->min_baseQ);
+ bcr = calloc(n, sizeof(bcf_callret1_t));
+ } else if (conf->flag & MPLP_VCF) {
ma = mc_init(n);
mc_init_prior(ma, conf->prior_type, conf->theta);
}
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
ref_tid = tid;
}
- if (conf->vcf) {
- double f0, f, fpost, pref = -1.0; // the reference allele frequency
- int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0;
+ if (conf->flag & MPLP_GLF) {
+ int _ref0, ref16;
+ bcf1_t *b = calloc(1, sizeof(bcf1_t));
+ _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+ ref16 = bam_nt16_table[_ref0];
+ for (i = 0; i < n; ++i)
+ bcf_call_glfgen(n_plp[i], plp[i], ref16, bca, bcr + i);
+ bcf_call_combine(n, bcr, ref16, &bc);
+ bcf_call2bcf(tid, pos, &bc, b);
+ bcf_write(bp, b);
+ //fprintf(stderr, "%d,%d,%d\n", b->tid, b->pos, b->l_str);
+ bcf_destroy(b);
+ } else 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;
_ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
_ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
- f = f0 = fpost = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
- if (f >= 0.0) {
- double q, flast = f;
- 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;
- }
- pref = mc_ref_prob(ma);
- fpost = mc_freq_post(ma);
- if (1. - f < 1e-4) f = 1.;
- if (1. - fpost < 1e-4) fpost = 1.;
- is_var = (pref < .5);
- q = is_var? pref : 1. - pref;
+ 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->var_only && !is_var) continue;
+ 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 (is_var) {
- if (_ref0 == _ref) putchar("ACGTN"[_alt]);
- else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
+ putchar("ACGTN"[r.alt]);
+ if (r.alt2 >= 0 && r.alt2 < 4) printf(",%c", "ACGT"[r.alt2]);
} else putchar('.');
printf("\t%d\t", qref);
- if (f0 < 0.) printf("Q13\t");
+ if (!tot) printf("Q13\t");
+ else if (r.f_exp < 0.) printf("FPE\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", depth, rms_q);
- if (fpost >= 0. && fpost <= 1.) printf(";AF=%.3lg", 1. - fpost);
- if (f >= 0. && f <= 1.) printf(";AFEM=%.3lg", 1. - f);
+ 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);
+ }
printf("\tGT:GQ:DP");
- if (fpost >= 0. && fpost <= 1.) {
+ if (tot) {
for (i = 0; i < n; ++i) {
- int x = mc_call_gt(ma, fpost, 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');
}
}
+ bcf_close(bp);
+ if (conf->flag&MPLP_VCF) mc_dump_afs(ma);
if (hash) { // free the hash table
khint_t k;
for (k = kh_begin(hash); k < kh_end(hash); ++k)
if (kh_exist(hash, k)) free(kh_val(hash, k));
kh_destroy(64, hash);
}
+ bcf_call_destroy(bca); free(bc.PL); free(bcr);
mc_destroy(ma);
bam_mplp_destroy(iter);
bam_header_destroy(h);
mplp.max_mq = 60;
mplp.prior_type = MC_PTYPE_FULL;
mplp.theta = 1e-3;
- while ((c = getopt(argc, argv, "f:r:l:VvM:q:t:2")) >= 0) {
+ mplp.min_baseQ = 13;
+ while ((c = getopt(argc, argv, "gvVcFSP:f:r:l:VM:q:t:Q:u")) >= 0) {
switch (c) {
case 't': mplp.theta = atof(optarg); break;
- case '2': mplp.prior_type = MC_PTYPE_COND2; 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.var_only = 1; break;
- case 'V': mplp.vcf = 1; break;
+ case 'g': mplp.flag |= MPLP_GLF; break;
+ case 'V':
+ case 'c': mplp.flag |= MPLP_VCF; break;
+ case 'F': mplp.flag |= MPLP_AFALL; break;
+ case 'v': mplp.flag |= MPLP_VAR; break;
+ case 'u': mplp.flag |= MPLP_NO_COMP; break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
+ case 'Q': mplp.min_baseQ = atoi(optarg); break;
}
}
+ if (mplp.flag&MPLP_GLF) mplp.flag &= ~MPLP_VCF;
if (argc == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\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, " -V generate VCF output (SNP calling)\n");
+ fprintf(stderr, " -P STR prior: full, flat, cond2 [full]\n");
+ fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
+ fprintf(stderr, " -c generate VCF output (consensus calling)\n");
+ fprintf(stderr, " -g generate GLF output\n");
fprintf(stderr, " -v show variant sites only\n");
- fprintf(stderr, " -2 conditional prior\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
return 1;
projects / samtools.git / blobdiff