X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=0aa44f5853e3126d8d403b05b1f9d45335081b61;hb=c350a570e955d5b4c2c13f607b7442df6d332c67;hp=f6381c3d67d9da414bfdd40b4df7a7db9693199a;hpb=8ec3e2c3435d8d000ff5edbeb250e8b46c324eca;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index f6381c3..0aa44f5 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -6,93 +6,8 @@ #include #include "sam.h" #include "faidx.h" -#include "bam_maqcns.h" -#include "khash.h" -#include "glf.h" #include "kstring.h" -typedef int *indel_list_t; -KHASH_MAP_INIT_INT64(64, indel_list_t) - -#define BAM_PLF_SIMPLE 0x01 -#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 -#define BAM_PLF_NOBAQ 0x400 - -typedef struct { - bam_header_t *h; - bam_maqcns_t *c; - bam_maqindel_opt_t *ido; - faidx_t *fai; - khash_t(64) *hash; - 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 -} pu_data_t; - -char **__bam_get_lines(const char *fn, int *_n); -void bam_init_header_hash(bam_header_t *header); -int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); - -static khash_t(64) *load_pos(const char *fn, bam_header_t *h) -{ - char **list; - int i, j, n, *fields, max_fields; - khash_t(64) *hash; - bam_init_header_hash(h); - list = __bam_get_lines(fn, &n); - hash = kh_init(64); - max_fields = 0; fields = 0; - for (i = 0; i < n; ++i) { - char *str = list[i]; - int chr, n_fields, ret; - khint_t k; - uint64_t x; - n_fields = ksplit_core(str, 0, &max_fields, &fields); - if (n_fields < 2) continue; - chr = bam_get_tid(h, str + fields[0]); - if (chr < 0) { - fprintf(stderr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]); - continue; - } - x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1); - k = kh_put(64, hash, x, &ret); - if (ret == 0) { - fprintf(stderr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]); - continue; - } - kh_val(hash, k) = 0; - if (n_fields > 2) { - // count - for (j = 2; j < n_fields; ++j) { - char *s = str + fields[j]; - if ((*s != '+' && *s != '-') || !isdigit(s[1])) break; - } - if (j > 2) { // update kh_val() - int *q, y, z; - q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int)); - q[0] = j - 2; z = j; y = 1; - for (j = 2; j < z; ++j) - q[y++] = atoi(str + fields[j]); - } - } - free(str); - } - free(list); free(fields); - return hash; -} - static inline int printw(int c, FILE *fp) { char buf[16]; @@ -108,75 +23,6 @@ static inline int printw(int c, FILE *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) -{ - pu_data_t *d = (pu_data_t*)data; - bam_maqindel_ret_t *r = 0; - int rb, *proposed_indels = 0; - glf1_t *g; - glf3_t *g3; - - if (d->fai == 0) { - fprintf(stderr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n"); - exit(1); - } - if (d->hash) { // only output a list of sites - 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); - } - g3 = glf3_init1(); - if (d->fai && (int)tid != d->tid) { - if (d->ref) { // then write the end mark - g3->rtype = GLF3_RTYPE_END; - glf3_write1(d->fp_glf, g3); - } - glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference - free(d->ref); - d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len); - d->tid = tid; - d->last_pos = 0; - } - rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N'; - g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c); - memcpy(g3, g, sizeof(glf1_t)); - g3->rtype = GLF3_RTYPE_SUB; - g3->offset = pos - d->last_pos; - d->last_pos = pos; - glf3_write1(d->fp_glf, g3); - 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; - if (min > r->gl[0]) min = r->gl[0]; - if (min > r->gl[1]) min = r->gl[1]; - g3->ref_base = 0; - g3->rtype = GLF3_RTYPE_INDEL; - memset(g3->lk, 0, 10); - g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255; - g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255; - g3->lk[2] = het - min < 255? het - min : 255; - g3->offset = 0; - g3->indel_len[0] = r->indel1; - g3->indel_len[1] = r->indel2; - g3->min_lk = min < 255? min : 255; - g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1; - g3->indel_seq[0] = strdup(r->s[0]+1); - g3->indel_seq[1] = strdup(r->s[1]+1); - glf3_write1(d->fp_glf, g3); - bam_maqindel_ret_destroy(r); - } - free(g); - glf3_destroy1(g3); - return 0; -} - static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref) { int j; @@ -212,317 +58,6 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons 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, 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 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); - } - // update d->ref if necessary - if (d->fai && (int)tid != d->tid) { - free(d->ref); - 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 { - 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; - 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 != 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 - 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) { - 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 - printw(n, stdout); putchar('\t'); - for (i = 0; i < n; ++i) - pileup_seq(pu + i, pos, d->len, d->ref); - // finalize rms_mapq - if (d->format & BAM_PLF_CNS) { - for (i = rms_aux = 0; i < n; ++i) { - const bam_pileup1_t *p = pu + i; - int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ; - rms_aux += tmp * tmp; - } - 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) { - int c = pu[i].b->core.qual + 33; - if (c > 126) c = 126; - 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; - printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(','); - } - } - putchar('\n'); - // 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, 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\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; -} - -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 = 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: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; - 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); 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 (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, " -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, " -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 [%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 compute the consensus sequence\n"); - fprintf(stderr, " -v print variants only (for -c)\n"); - 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"); - fprintf(stderr, "Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!\n\n"); - 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 - glf3_header_t *h; - h = glf3_header_init(); - d->fp_glf = bgzf_fdopen(fileno(stdout), "w"); - glf3_header_write(d->fp_glf, h); - glf3_header_destroy(h); - } - 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 = 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; - } - d->h = fp->header; - if (fn_pos) d->hash = load_pos(fn_pos, d->h); - { // 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; - if ((int)b->core.tid < 0) break; - // 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 - } - - // free - if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf); - if (fn_pos) { // free the hash table - khint_t k; - for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k) - if (kh_exist(d->hash, k)) free(kh_val(d->hash, k)); - kh_destroy(64, d->hash); - } - free(fn_pos); free(fn_list); free(fn_fa); - if (d->fai) fai_destroy(d->fai); - bam_maqcns_destroy(d->c); - free(d->ido); free(d->ref); free(d); - return 0; -} - -/*********** - * mpileup * - ***********/ - #include #include "bam2bcf.h" #include "sample.h"