X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=285477050d19f489d7be34722846eca8e6407e14;hb=d73a1b3b94255044787c0e4bfeba37df66e99770;hp=1d5ea5a82da2076217deb9bf224a5ed12b0655ef;hpb=b0ed19dc2d8fb84998d41d6c3588611185707137;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index 1d5ea5a..2854770 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -1,9 +1,11 @@ +#include #include #include #include #include "sam.h" #include "faidx.h" #include "bam_maqcns.h" +#include "bam_mcns.h" #include "khash.h" #include "glf.h" #include "kstring.h" @@ -15,6 +17,12 @@ KHASH_MAP_INIT_INT64(64, indel_list_t) #define BAM_PLF_CNS 0x02 #define BAM_PLF_INDEL_ONLY 0x04 #define BAM_PLF_GLF 0x08 +#define BAM_PLF_VAR_ONLY 0x10 +#define BAM_PLF_2ND 0x20 +#define BAM_PLF_RANBASE 0x40 +#define BAM_PLF_1STBASE 0x80 +#define BAM_PLF_ALLBASE 0x100 +#define BAM_PLF_READPOS 0x200 typedef struct { bam_header_t *h; @@ -25,6 +33,7 @@ typedef struct { uint32_t format; int tid, len, last_pos; int mask; + 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 } pu_data_t; @@ -118,9 +127,12 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, g3->offset = pos - d->last_pos; d->last_pos = pos; glf3_write1(d->fp_glf, g3); - if (proposed_indels) - r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); - else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + if (pos < d->len) { + int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth; + if (proposed_indels) + r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); + else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0); + } if (r) { // then write indel line int het = 3 * n, min; min = het; @@ -147,81 +159,146 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, return 0; } +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_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'; + if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.'; + else c = bam1_strand(p->b)? tolower(c) : toupper(c); + putchar(c); + if (p->indel > 0) { + printf("+%d", p->indel); + 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); + 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('*'); + if (p->is_tail) putchar('$'); +} + static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data) { pu_data_t *d = (pu_data_t*)data; bam_maqindel_ret_t *r = 0; - int i, j, rb, rms_mapq = -1, max_mapq = 0, *proposed_indels = 0; - uint32_t x; + int i, rb, rms_mapq = -1, *proposed_indels = 0; + uint64_t rms_aux; + uint32_t cns = 0; + // if GLF is required, suppress -c completely if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data); - if (d->hash) { // only output a list of sites + // if d->hash is initialized, only output the sites in the hash table + if (d->hash) { khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos); if (k == kh_end(d->hash)) return 0; proposed_indels = kh_val(d->hash, k); } - if (d->fai && (int)tid != d->tid) { // then update d->ref + // update d->ref if necessary + if (d->fai && (int)tid != d->tid) { free(d->ref); - d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len); + d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &d->len); d->tid = tid; } rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N'; + // when the indel-only mode is asked for, return if no reads mapped with indels if (d->format & BAM_PLF_INDEL_ONLY) { for (i = 0; i < n; ++i) if (pu[i].indel != 0) break; if (i == n) return 0; } + // call the consensus and indel + if (d->format & BAM_PLF_CNS) { // call consensus + if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call + const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n); + int q = bam1_qual(p->b)[p->qpos]; + int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos); + cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8; + } else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases + uint64_t rmsQ = 0; + uint32_t b = 0; + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + b |= bam1_seqi(bam1_seq(p->b), p->qpos); + rmsQ += q * q; + } + 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); + } + 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; + if (proposed_indels) // the first element gives the size of the array + r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); + else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0); + } + // 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 (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel + if (r) bam_maqindel_ret_destroy(r); + return 0; + } + } + } + // print the first 3 columns printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb); - if (d->format & BAM_PLF_CNS) { // consensus + // print consensus information if required + if (d->format & BAM_PLF_CNS) { int ref_q, rb4 = bam_nt16_table[rb]; - x = bam_maqcns_call(n, pu, d->c); ref_q = 0; - if (rb4 != 15 && x>>28 != 15 && x>>28 != rb4) { // a SNP - ref_q = ((x>>24&0xf) == rb4)? x>>8&0xff : (x>>8&0xff) + (x&0xff); + 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; } - printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff); - rms_mapq = x>>16&0xff; - } - if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { - if (proposed_indels) - r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1); - else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0); + 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); } - // pileup strings + // print pileup sequences printf("%d\t", n); + 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; - if (max_mapq < p->b->core.qual) max_mapq = p->b->core.qual; - if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33); - if (!p->is_del) { - int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; - if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.'; - else c = bam1_strand(p->b)? tolower(c) : toupper(c); - putchar(c); - if (p->indel > 0) { - printf("+%d", p->indel); - 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); - for (j = 1; j <= -p->indel; ++j) { - c = (d->ref && (int)pos+j < d->len)? d->ref[pos+j] : 'N'; - putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); - } - } - } else putchar('*'); - if (p->is_tail) putchar('$'); + int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; + rms_aux += tmp * tmp; + pileup_seq(p, pos, d->len, d->ref); } + // finalize rms_mapq + rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499); + if (rms_mapq < 0) rms_mapq = rms_aux; putchar('\t'); + // print quality for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pu + i; int c = bam1_qual(p->b)[p->qpos] + 33; if (c > 126) c = 126; putchar(c); } + if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities + const unsigned char *q; + putchar('\t'); + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + q = bam_aux_get(p->b, "E2"); + putchar(q? q[p->qpos + 1] : 'N'); + } + putchar('\t'); + for (i = 0; i < n; ++i) { + const bam_pileup1_t *p = pu + i; + q = bam_aux_get(p->b, "U2"); + putchar(q? q[p->qpos + 1] : '!'); + } + } + // print mapping quality if -s is flagged on the command line if (d->format & BAM_PLF_SIMPLE) { putchar('\t'); for (i = 0; i < n; ++i) { @@ -230,16 +307,28 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p putchar(c); } } + // print read position + if (d->format & BAM_PLF_READPOS) { + putchar('\t'); + 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)); + } + } putchar('\n'); - if (r) { // then print indel line + // print the indel line if r has been calculated. This only happens if: + // a) -c or -i are flagged, AND b) the reference sequence is available + if (r) { printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1); if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]); else printf("%s/%s\t", r->s[0], r->s[1]); printf("%d\t%d\t", r->q_cns, r->q_ref); - printf("%d\t%d\t", rms_mapq >= 0? rms_mapq : max_mapq, n); + printf("%d\t%d\t", rms_mapq, n); printf("%s\t%s\t", r->s[0], r->s[1]); //printf("%d\t%d\t", r->gl[0], r->gl[1]); - printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti); + printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti); + printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi); bam_maqindel_ret_destroy(r); } return 0; @@ -247,40 +336,63 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p int bam_pileup(int argc, char *argv[]) { - int c; + 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->c = bam_maqcns_init(); + d->c->is_soap = 1; // change the default model d->ido = bam_maqindel_opt_init(); - while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:")) >= 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->is_soap = 0; 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; case 'i': d->format |= BAM_PLF_INDEL_ONLY; break; + case 'v': d->format |= BAM_PLF_VAR_ONLY; break; case 'm': d->mask = strtol(optarg, 0, 0); break; case 'g': d->format |= BAM_PLF_GLF; break; + case '2': d->format |= BAM_PLF_2ND; break; + case 'P': d->format |= BAM_PLF_READPOS; break; case 'I': d->ido->q_indel = atoi(optarg); break; case 'G': d->ido->r_indel = atof(optarg); break; + case 'S': is_SAM = 1; break; + case 'R': + if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE; + else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE; + else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE; + else fprintf(stderr, "[bam_pileup] unrecognized -R\n"); + break; default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1; } } + 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, " -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 (assume the input is in SAM)\n"); + 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, " -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); fprintf(stderr, " -N INT number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap); @@ -291,6 +403,7 @@ int bam_pileup(int argc, char *argv[]) free(fn_list); free(fn_fa); free(d); return 1; } + if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS; if (fn_fa) d->fai = fai_load(fn_fa); if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling if (d->format & BAM_PLF_GLF) { // for glf output @@ -302,9 +415,11 @@ int bam_pileup(int argc, char *argv[]) } if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY))) fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n"); + if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa); + { samfile_t *fp; - fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); + fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); if (fp == 0 || fp->header == 0) { fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n"); return 1; @@ -329,3 +444,222 @@ int bam_pileup(int argc, char *argv[]) free(d->ido); free(d->ref); free(d); return 0; } + +/*********** + * mpileup * + ***********/ + +typedef struct { + int vcf, max_mq, min_mq, var_only; + char *reg, *fn_pos; + faidx_t *fai; + kh_64_t *hash; +} mplp_conf_t; + +typedef struct { + bamFile fp; + bam_iter_t iter; + int min_mq; +} mplp_aux_t; + +static int mplp_func(void *data, bam1_t *b) +{ + mplp_aux_t *ma = (mplp_aux_t*)data; + int ret; + do { + 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); + return ret; +} + +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; + char *ref; + khash_t(64) *hash = 0; + // allocate + 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; + data[i] = calloc(1, sizeof(mplp_aux_t)); + data[i]->min_mq = conf->min_mq; + data[i]->fp = bam_open(fn[i], "r"); + h_tmp = bam_header_read(data[i]->fp); + if (conf->reg) { + int beg, end; + bam_index_t *idx; + idx = bam_index_load(fn[i]); + if (idx == 0) { + fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1); + exit(1); + } + if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) { + fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1); + exit(1); + } + if (i == 0) beg0 = beg, end0 = end; + data[i]->iter = bam_iter_query(idx, tid, beg, end); + bam_index_destroy(idx); + } + if (i == 0) h = h_tmp; + else { + // FIXME: to check consistency + bam_header_destroy(h_tmp); + } + } + if (conf->fn_pos) hash = load_pos(conf->fn_pos, h); + // write the VCF header + if (conf->vcf) { + kstring_t s; + s.l = s.m = 0; s.s = 0; + puts("##fileformat=VCFv4.0"); + 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->vcf) ma = mc_init(n); + 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); + ref_tid = tid; + } + if (conf->vcf) { + double f0, f, pref = -1.0; // the reference allele frequency + int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0; + uint64_t sqr_sum; + _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 q, flast = f; + for (j = 0; j < 10; ++j){ + f = mc_freq_iter(flast, ma); + if (fabs(f - flast) < 1e-3) break; + flast = f; + } + pref = mc_ref_prob(ma); + is_var = (pref < .5); + q = is_var? pref : 1. - pref; + 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; + 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]); + } else putchar('.'); + printf("\t%d\t", qref); + if (f0 < 0.) printf("Q13\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;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f); + printf("\tGT:GQ:DP"); + // output genotype information; FIXME: to be implmented... + for (i = 0; i < n; ++i) { + int x = mc_call_gt(ma, f, i); + printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]); + } + putchar('\n'); + } 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'); + } + } + 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); + } + mc_destroy(ma); + bam_mplp_destroy(iter); + bam_header_destroy(h); + for (i = 0; i < n; ++i) { + bam_close(data[i]->fp); + if (data[i]->iter) bam_iter_destroy(data[i]->iter); + free(data[i]); + } + free(data); free(plp); free(ref); free(n_plp); + return 0; +} + +int bam_mpileup(int argc, char *argv[]) +{ + int c; + mplp_conf_t mplp; + memset(&mplp, 0, sizeof(mplp_conf_t)); + mplp.max_mq = 60; + while ((c = getopt(argc, argv, "f:r:l:VvM:q:")) >= 0) { + switch (c) { + 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 '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"); + return 1; + } + mpileup(&mplp, argc - optind, argv + optind); + free(mplp.reg); + if (mplp.fai) fai_destroy(mplp.fai); + return 0; +}