d->max_depth = 0;
d->tid = -1; d->mask = BAM_DEF_MASK;
d->c = bam_maqcns_init();
+ d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model
d->ido = bam_maqindel_opt_init();
- while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:P")) >= 0) {
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PA")) >= 0) {
switch (c) {
- case 'a': d->c->is_soap = 1; break;
+ case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break;
+ case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break;
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'l': fn_pos = strdup(optarg); break;
case 'f': fn_fa = strdup(optarg); break;
case 'T': d->c->theta = atof(optarg); break;
case 'N': d->c->n_hap = atoi(optarg); break;
- case 'r': d->c->het_rate = atof(optarg); break;
+ case 'r': d->c->het_rate = atof(optarg); d->ido->r_snp = d->c->het_rate; break;
case 'M': d->c->cap_mapQ = atoi(optarg); break;
case 'd': d->max_depth = atoi(optarg); break;
case 'c': d->format |= BAM_PLF_CNS; break;
default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
}
}
+ if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
+ if (d->c->theta > 1.0) d->c->theta = 1.0;
if (fn_list) is_SAM = 1;
if (optind == argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
fprintf(stderr, " -S the input is in SAM\n");
- fprintf(stderr, " -a use the SOAPsnp model for SNP calling\n");
+ fprintf(stderr, " -A use the MAQ model for SNP calling\n");
fprintf(stderr, " -2 output the 2nd best call and quality\n");
fprintf(stderr, " -i only show lines/consensus with indels\n");
fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
fprintf(stderr, " -t FILE list of reference sequences (force -S)\n");
fprintf(stderr, " -l FILE list of sites at which pileup is output\n");
fprintf(stderr, " -f FILE reference sequence in the FASTA format\n\n");
- fprintf(stderr, " -c output the maq consensus sequence\n");
+ fprintf(stderr, " -c output the SOAPsnp consensus sequence\n");
fprintf(stderr, " -v print variants only (for -c)\n");
fprintf(stderr, " -g output in the GLFv3 format (suppressing -c/-i/-s)\n");
fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
* mpileup *
***********/
+#include <assert.h>
+#include "bam2bcf.h"
+#include "sample.h"
+
+#define MPLP_GLF 0x10
+#define MPLP_NO_COMP 0x20
+#define MPLP_NO_ORPHAN 0x40
+#define MPLP_REALN 0x80
+#define MPLP_NO_HALFTRIM 0x100
+
typedef struct {
- char *reg;
+ int max_mq, min_mq, flag, min_baseQ;
+ double theta;
+ char *reg, *fn_pos;
faidx_t *fai;
+ kh_64_t *hash;
} mplp_conf_t;
typedef struct {
bamFile fp;
- bam_iterf_t iter;
+ bam_iter_t iter;
+ int min_mq, flag;
+ char *ref;
} mplp_aux_t;
+typedef struct {
+ int n;
+ int *n_plp, *m_plp;
+ bam_pileup1_t **plp;
+} mplp_pileup_t;
+
static int mplp_func(void *data, bam1_t *b)
{
+ extern int bam_realn(bam1_t *b, const char *ref);
mplp_aux_t *ma = (mplp_aux_t*)data;
- if (ma->iter) return bam_iterf_read(ma->fp, ma->iter, b);
- return bam_read1(ma->fp, b);
+ int ret, cond = 0;
+ do {
+ cond = 0;
+ ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
+ if (ret < 0) break;
+ if (b->core.qual < ma->min_mq) cond = 1;
+ else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) cond = 1;
+ if (ma->ref && !cond && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
+ } while (cond);
+ return ret;
+}
+
+static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
+ int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp)
+{
+ int i, j;
+ memset(m->n_plp, 0, m->n * sizeof(int));
+ for (i = 0; i < n; ++i) {
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ uint8_t *q;
+ int id = -1;
+ q = bam_aux_get(p->b, "RG");
+ if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
+ if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
+ assert(id >= 0 && id < m->n);
+ if (m->n_plp[id] == m->m_plp[id]) {
+ m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+ m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+ }
+ m->plp[id][m->n_plp[id]++] = *p;
+ }
+ }
}
static int mpileup(mplp_conf_t *conf, int n, char **fn)
bam_mplp_t iter;
bam_header_t *h = 0;
char *ref;
- // allocate
+ khash_t(64) *hash = 0;
+
+ bcf_callaux_t *bca = 0;
+ bcf_callret1_t *bcr = 0;
+ bcf_call_t bc;
+ bcf_t *bp = 0;
+ bcf_hdr_t *bh = 0;
+
+ bam_sample_t *sm = 0;
+ kstring_t buf;
+ mplp_pileup_t gplp;
+
+ memset(&gplp, 0, sizeof(mplp_pileup_t));
+ memset(&buf, 0, sizeof(kstring_t));
+ memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(void*));
plp = calloc(n, sizeof(void*));
n_plp = calloc(n, sizeof(int*));
+ sm = bam_smpl_init();
+
// read the header and initialize data
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
+ data[i]->min_mq = conf->min_mq;
+ data[i]->flag = conf->flag;
data[i]->fp = bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
+ bam_smpl_add(sm, fn[i], h_tmp->text);
if (conf->reg) {
int beg, end;
bam_index_t *idx;
exit(1);
}
if (i == 0) beg0 = beg, end0 = end;
- data[i]->iter = bam_iterf_query(idx, tid, beg, end);
+ data[i]->iter = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
if (i == 0) h = h_tmp;
bam_header_destroy(h_tmp);
}
}
- // mpileup
+ gplp.n = sm->n;
+ gplp.n_plp = calloc(sm->n, sizeof(int));
+ gplp.m_plp = calloc(sm->n, sizeof(int));
+ gplp.plp = calloc(sm->n, sizeof(void*));
+
+ fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+ if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
+ // write the VCF header
+ if (conf->flag & MPLP_GLF) {
+ kstring_t s;
+ bh = calloc(1, sizeof(bcf_hdr_t));
+ 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);
+ }
+ bh->l_nm = s.l;
+ bh->name = malloc(s.l);
+ memcpy(bh->name, s.s, s.l);
+ s.l = 0;
+ for (i = 0; i < sm->n; ++i) {
+ kputs(sm->smpl[i], &s); kputc('\0', &s);
+ }
+ bh->l_smpl = s.l;
+ bh->sname = malloc(s.l);
+ memcpy(bh->sname, s.s, s.l);
+ bh->l_txt = 0;
+ free(s.s);
+ bcf_hdr_sync(bh);
+ bcf_hdr_write(bp, bh);
+ bca = bcf_call_init(-1., conf->min_baseQ);
+ bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+ }
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->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+ if (hash) {
+ khint_t k;
+ k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
+ if (k == kh_end(hash)) continue;
+ }
if (tid != ref_tid) {
free(ref);
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+ for (i = 0; i < n; ++i) data[i]->ref = ref;
ref_tid = tid;
}
- 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) {
- int j;
- printf("\t%d\t", n_plp[i]);
- if (n_plp[i] == 0) printf("*\t*");
- else {
- for (j = 0; j < n_plp[i]; ++j)
- pileup_seq(plp[i] + j, pos, ref_len, ref);
- putchar('\t');
- for (j = 0; j < n_plp[i]; ++j) {
- const bam_pileup1_t *p = plp[i] + j;
- int c = bam1_qual(p->b)[p->qpos] + 33;
- if (c > 126) c = 126;
- putchar(c);
+ if (conf->flag & MPLP_GLF) {
+ int _ref0, ref16;
+ bcf1_t *b = calloc(1, sizeof(bcf1_t));
+ group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
+ _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+ ref16 = bam_nt16_table[_ref0];
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+ bcf_call_combine(gplp.n, bcr, ref16, &bc);
+ bcf_call2bcf(tid, pos, &bc, b);
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ } 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) {
+ int j;
+ printf("\t%d\t", n_plp[i]);
+ if (n_plp[i] == 0) printf("*\t*");
+ else {
+ for (j = 0; j < n_plp[i]; ++j)
+ pileup_seq(plp[i] + j, pos, ref_len, ref);
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ int c = bam1_qual(p->b)[p->qpos] + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
}
}
+ putchar('\n');
}
- putchar('\n');
}
+
+ bcf_close(bp);
+ bam_smpl_destroy(sm); free(buf.s);
+ for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+ free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+ 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_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
bam_mplp_destroy(iter);
bam_header_destroy(h);
for (i = 0; i < n; ++i) {
bam_close(data[i]->fp);
- if (data[i]->iter) bam_iterf_destroy(data[i]->iter);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
free(data[i]);
}
free(data); free(plp); free(ref); free(n_plp);
int c;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
- while ((c = getopt(argc, argv, "f:r:")) >= 0) {
+ mplp.max_mq = 60;
+ mplp.theta = 1e-3;
+ mplp.min_baseQ = 13;
+ while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORH")) >= 0) {
switch (c) {
+ case 't': mplp.theta = atof(optarg); break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
break;
- case 'r': mplp.reg = strdup(optarg);
+ case 'r': mplp.reg = strdup(optarg); break;
+ case 'l': mplp.fn_pos = strdup(optarg); break;
+ case 'g': mplp.flag |= MPLP_GLF; break;
+ case 'u': mplp.flag |= MPLP_NO_COMP; break;
+ case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN | MPLP_NO_HALFTRIM; break;
+ case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
+ case 'H': mplp.flag |= MPLP_NO_HALFTRIM; break;
+ case 'R': mplp.flag |= MPLP_REALN; 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 (argc == 1) {
- fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] 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 min base quality [%d]\n", mplp.min_baseQ);
+ 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, " -g generate BCF output\n");
+ fprintf(stderr, " -u do not compress BCF output\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;
}
mpileup(&mplp, argc - optind, argv + optind);
projects / samtools.git / blobdiff