X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=cf98f69565ee6d52176df5ca5c9d14a44d2ef3e6;hb=253dbf083d8a84721ae6ac63af786c8dcf566ecb;hp=aef10d38e37797bd24e728e3dd13955e92dc7b64;hpb=5c4ef838b286eeb6fffc7c41ffbb776281963c8e;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index aef10d3..cf98f69 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -5,8 +5,6 @@ #include "sam.h" #include "faidx.h" #include "bam_maqcns.h" -#include "bam_mcns.h" -#include "bam2bcf.h" #include "khash.h" #include "glf.h" #include "kstring.h" @@ -24,6 +22,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t) #define BAM_PLF_1STBASE 0x80 #define BAM_PLF_ALLBASE 0x100 #define BAM_PLF_READPOS 0x200 +#define BAM_PLF_NOBAQ 0x400 typedef struct { bam_header_t *h; @@ -34,6 +33,7 @@ typedef struct { uint32_t format; int tid, len, last_pos; int mask; + int capQ_thres, min_baseQ; int max_depth; // for indel calling, ignore reads with the depth too high. 0 for unlimited char *ref; glfFile fp_glf; // for glf output only @@ -91,6 +91,21 @@ static khash_t(64) *load_pos(const char *fn, bam_header_t *h) return hash; } +static inline int printw(int c, FILE *fp) +{ + char buf[16]; + int l, x; + if (c == 0) return fputc('0', fp); + for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0'; + if (c < 0) buf[l++] = '-'; + buf[l] = 0; + for (x = 0; x < l/2; ++x) { + int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y; + } + fputs(buf, fp); + return 0; +} + // an analogy to pileup_func() below static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data) { @@ -162,7 +177,10 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref) { - if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33); + if (p->is_head) { + putchar('^'); + putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33); + } if (!p->is_del) { int j, rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; rb = (ref && pos < ref_len)? ref[pos] : 'N'; @@ -170,19 +188,19 @@ static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char else c = bam1_strand(p->b)? tolower(c) : toupper(c); putchar(c); if (p->indel > 0) { - printf("+%d", p->indel); + putchar('+'); printw(p->indel, stdout); for (j = 1; j <= p->indel; ++j) { c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)]; putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); } } else if (p->indel < 0) { - printf("%d", p->indel); + printw(p->indel, stdout); for (j = 1; j <= -p->indel; ++j) { c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N'; putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); } } - } else putchar('*'); + } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*'); if (p->is_tail) putchar('$'); } @@ -234,7 +252,11 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p } rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499); cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8; - } else cns = bam_maqcns_call(n, pu, d->c); + } else { + glf1_t *g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c); + cns = g->depth == 0? (0xfu<<28 | 0xf<<24) : glf2cns(g, (int)(d->c->q_r + .499)); + free(g); + } } if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth; @@ -244,7 +266,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p } // when only variant sites are asked for, test if the site is a variant if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) { - if (!(bam_nt16_table[rb] != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP + if (!(bam_nt16_table[rb] != 15 && cns>>28 != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel if (r) bam_maqindel_ret_destroy(r); return 0; @@ -252,20 +274,17 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p } } // print the first 3 columns - printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb); + fputs(d->h->target_name[tid], stdout); putchar('\t'); + printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t'); // print consensus information if required if (d->format & BAM_PLF_CNS) { - int ref_q, rb4 = bam_nt16_table[rb]; - ref_q = 0; - if (rb4 != 15 && cns>>28 != 15 && cns>>28 != rb4) { // a SNP - ref_q = ((cns>>24&0xf) == rb4)? cns>>8&0xff : (cns>>8&0xff) + (cns&0xff); - if (ref_q > 255) ref_q = 255; - } - rms_mapq = cns>>16&0xff; - printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, ref_q, rms_mapq); + putchar(bam_nt16_rev_table[cns>>28]); putchar('\t'); + printw(cns>>8&0xff, stdout); putchar('\t'); + printw(cns&0xff, stdout); putchar('\t'); + printw(cns>>16&0xff, stdout); putchar('\t'); } // print pileup sequences - printf("%d\t", n); + printw(n, stdout); putchar('\t'); rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pu + i; @@ -314,7 +333,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p for (i = 0; i < n; ++i) { int x = pu[i].qpos; int l = pu[i].b->core.l_qseq; - printf("%d,", x < l/2? x+1 : -((l-1)-x+1)); + printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(','); } } putchar('\n'); @@ -340,13 +359,15 @@ int bam_pileup(int argc, char *argv[]) int c, is_SAM = 0; char *fn_list = 0, *fn_fa = 0, *fn_pos = 0; pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t)); - d->max_depth = 0; - d->tid = -1; d->mask = BAM_DEF_MASK; + d->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13; 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:PA")) >= 0) { + while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PAQ:C:B")) >= 0) { switch (c) { + case 'Q': d->c->min_baseQ = atoi(optarg); break; + case 'C': d->capQ_thres = atoi(optarg); break; + case 'B': d->format |= BAM_PLF_NOBAQ; 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; @@ -377,29 +398,34 @@ int bam_pileup(int argc, char *argv[]) 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] |\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 MAQ model for SNP calling\n"); + fprintf(stderr, " -B disable BAQ computation\n"); + fprintf(stderr, " -A use the original MAQ model for SNP calling (DEPRECATED)\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, " -Q INT min base quality (possibly capped by BAQ) [%d]\n", d->c->min_baseQ); + fprintf(stderr, " -C INT coefficient for adjusting mapQ of poor mappings [%d]\n", d->capQ_thres); + fprintf(stderr, " -m INT filtering reads with bits in INT [0x%x]\n", d->mask); fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ); - fprintf(stderr, " -d INT limit maximum depth for indels [unlimited]\n"); + fprintf(stderr, " -d INT limit maximum depth for indels [%d]\n", d->max_depth); 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 SOAPsnp consensus sequence\n"); + fprintf(stderr, " -c compute the 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); - fprintf(stderr, " -N INT number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap); - fprintf(stderr, " -r FLOAT prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate); - fprintf(stderr, " -G FLOAT prior of an indel between two haplotypes (for -c/-g) [%f]\n", d->ido->r_indel); - fprintf(stderr, " -I INT phred prob. of an indel in sequencing/prep. (for -c/-g) [%d]\n", d->ido->q_indel); + fprintf(stderr, " -g output in the GLFv3 format (DEPRECATED)\n"); + fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c) [%.4g]\n", d->c->theta); + fprintf(stderr, " -N INT number of haplotypes in the sample (for -c) [%d]\n", d->c->n_hap); + fprintf(stderr, " -r FLOAT prior of a difference between two haplotypes (for -c) [%.4g]\n", d->c->het_rate); + fprintf(stderr, " -G FLOAT prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel); + fprintf(stderr, " -I INT phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel); fprintf(stderr, "\n"); free(fn_list); free(fn_fa); free(d); return 1; @@ -427,7 +453,42 @@ int bam_pileup(int argc, char *argv[]) } d->h = fp->header; if (fn_pos) d->hash = load_pos(fn_pos, d->h); - sampileup(fp, d->mask, pileup_func, d); + { // run pileup + extern int bam_prob_realn(bam1_t *b, const char *ref); + extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); + bam1_t *b; + int ret, tid, pos, n_plp; + bam_plp_t iter; + const bam_pileup1_t *plp; + b = bam_init1(); + iter = bam_plp_init(0, 0); + bam_plp_set_mask(iter, d->mask); + while ((ret = samread(fp, b)) >= 0) { + int skip = 0; + // update d->ref if necessary + if (d->fai && (int)b->core.tid != d->tid) { + free(d->ref); + d->ref = faidx_fetch_seq(d->fai, d->h->target_name[b->core.tid], 0, 0x7fffffff, &d->len); + d->tid = b->core.tid; + } + if (d->ref && (d->format&BAM_PLF_CNS) && !(d->format&BAM_PLF_NOBAQ)) bam_prob_realn(b, d->ref); + if (d->ref && (d->format&BAM_PLF_CNS) && d->capQ_thres > 10) { + int q = bam_cap_mapQ(b, d->ref, d->capQ_thres); + if (q < 0) skip = 1; + else if (b->core.qual > q) b->core.qual = q; + } else if (b->core.flag&BAM_FUNMAP) skip = 1; + else if ((d->format&BAM_PLF_CNS) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; + if (skip) continue; + bam_plp_push(iter, b); + while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0) + pileup_func(tid, pos, n_plp, plp, d); + } + bam_plp_push(iter, 0); + while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0) + pileup_func(tid, pos, n_plp, plp, d); + bam_plp_destroy(iter); + bam_destroy1(b); + } samclose(fp); // d->h will be destroyed here } @@ -450,17 +511,17 @@ int bam_pileup(int argc, char *argv[]) * mpileup * ***********/ -#define MPLP_VCF 0x1 -#define MPLP_VAR 0x2 -#define MPLP_AFALL 0x8 +#include +#include "bam2bcf.h" +#include "sample.h" + #define MPLP_GLF 0x10 #define MPLP_NO_COMP 0x20 - -#define MPLP_AFS_BLOCK 0x10000 +#define MPLP_NO_ORPHAN 0x40 +#define MPLP_REALN 0x80 typedef struct { - int max_mq, min_mq, prior_type, flag, min_baseQ; - double theta; + int max_mq, min_mq, flag, min_baseQ, capQ_thres; char *reg, *fn_pos; faidx_t *fai; kh_64_t *hash; @@ -469,19 +530,63 @@ typedef struct { typedef struct { bamFile fp; bam_iter_t iter; - int min_mq; + int min_mq, flag, ref_id, capQ_thres; + 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); + extern int bam_prob_realn(bam1_t *b, const char *ref); + extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); mplp_aux_t *ma = (mplp_aux_t*)data; - int ret; + int ret, skip = 0; do { + int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); - } while (b->core.qual < ma->min_mq && ret >= 0); + if (ret < 0) break; + skip = 0; + if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref); + if (has_ref && ma->capQ_thres > 10) { + int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres); + if (q < 0) skip = 1; + else if (b->core.qual > q) b->core.qual = q; + } else if (b->core.flag&BAM_FUNMAP) skip = 1; + else if (b->core.qual < ma->min_mq) skip = 1; + else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; + } while (skip); 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) { mplp_aux_t **data; @@ -489,30 +594,37 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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; - mc_aux_t *ma = 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]->fp = bam_open(fn[i], "r"); + data[i]->flag = conf->flag; + data[i]->capQ_thres = conf->capQ_thres; + data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : 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; @@ -535,6 +647,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bam_header_destroy(h_tmp); } } + 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) { @@ -550,12 +668,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bh->name = malloc(s.l); memcpy(bh->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); + 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); @@ -564,33 +678,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) free(s.s); bcf_hdr_sync(bh); bcf_hdr_write(bp, bh); - } else if (conf->flag & MPLP_VCF) { - kstring_t s; - s.l = s.m = 0; s.s = 0; - puts("##fileformat=VCFv4.0"); - puts("##INFO="); - puts("##INFO="); - puts("##INFO="); - puts("##FILTER="); - puts("##FILTER="); - kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s); - for (i = 0; i < n; ++i) { - const char *p; - kputc('\t', &s); - if ((p = strstr(fn[i], ".bam")) != 0) - kputsn(fn[i], p - fn[i], &s); - else kputs(fn[i], &s); - } - puts(s.s); - free(s.s); - } - // mpileup - 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); + bcr = calloc(sm->n, sizeof(bcf_callret1_t)); } ref_tid = -1; ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); @@ -602,73 +691,23 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) if (k == kh_end(hash)) continue; } if (tid != ref_tid) { - free(ref); + free(ref); ref = 0; if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len); + for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } 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 < n; ++i) - bcf_call_glfgen(n_plp[i], plp[i], ref16, bca, bcr + i); - bcf_call_combine(n, bcr, ref16, &bc); + 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); - //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]]; - 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 (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 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]; - for (j = 0; j < n_plp[i]; ++j) { - int q = plp[i][j].b->core.qual; - if (q > conf->max_mq) q = conf->max_mq; - sqr_sum += q * q; - } - } - rms_q = (int)(sqrt((double)sqr_sum / depth) + .499); - 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); - } - 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) { @@ -690,8 +729,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) putchar('\n'); } } + bcf_close(bp); - if (conf->flag&MPLP_VCF) mc_dump_afs(ma); + 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) @@ -699,7 +741,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) kh_destroy(64, hash); } bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr); - mc_destroy(ma); bam_mplp_destroy(iter); bam_header_destroy(h); for (i = 0; i < n; ++i) { @@ -717,21 +758,10 @@ int bam_mpileup(int argc, char *argv[]) mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.max_mq = 60; - mplp.prior_type = MC_PTYPE_FULL; - mplp.theta = 1e-3; mplp.min_baseQ = 13; - while ((c = getopt(argc, argv, "gvVcFSP:f:r:l:VM:q:t:Q:u")) >= 0) { + mplp.capQ_thres = 0; + while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 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; @@ -739,17 +769,16 @@ int bam_mpileup(int argc, char *argv[]) case 'r': mplp.reg = strdup(optarg); break; case 'l': mplp.fn_pos = strdup(optarg); 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 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break; + case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break; + case 'O': mplp.flag |= MPLP_NO_ORPHAN; break; + case 'R': mplp.flag |= MPLP_REALN; break; + case 'C': mplp.capQ_thres = atoi(optarg); 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"); @@ -757,15 +786,12 @@ int bam_mpileup(int argc, char *argv[]) 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, " -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, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq); + fprintf(stderr, " -g generate BCF output\n"); + fprintf(stderr, " -u do not compress BCF output\n"); fprintf(stderr, "\n"); - fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n"); + fprintf(stderr, "Notes: Assuming diploid individuals.\n\n"); return 1; } mpileup(&mplp, argc - optind, argv + optind);