X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=80799e3b28af95208796424c31a4bf5b7dd24ba0;hb=63af098c78ef4163356c281e87bfb467adc8824d;hp=2afebeadf85bc2ee020e3c8aecd0209dccebc51d;hpb=d763698cc12d7daa7361d610db3c9c9e83e7655b;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index 2afebea..80799e3 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -5,7 +5,7 @@ #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" @@ -342,12 +342,12 @@ int bam_pileup(int argc, char *argv[]) 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->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) { switch (c) { - case 'a': d->c->is_soap = 1; break; - case 'A': d->c->is_soap = 0; 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; @@ -449,8 +449,12 @@ int bam_pileup(int argc, char *argv[]) * mpileup * ***********/ +#define MPLP_GLF 0x10 +#define MPLP_NO_COMP 0x20 + typedef struct { - int vcf, max_mq, min_mq, var_only; + int max_mq, min_mq, flag, min_baseQ; + double theta; char *reg, *fn_pos; faidx_t *fai; kh_64_t *hash; @@ -475,17 +479,24 @@ static int mplp_func(void *data, bam1_t *b) 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 + + bcf_callaux_t *bca = 0; + bcf_callret1_t *bcr = 0; + bcf_call_t bc; + bcf_t *bp = 0; + bcf_hdr_t *bh = 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; @@ -517,23 +528,39 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) } 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; + bh = calloc(1, sizeof(bcf_hdr_t)); s.l = s.m = 0; s.s = 0; - puts("##fileformat=VCFv4.0"); - kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s); + 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 < 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); + kputc('\0', &s); } - puts(s.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); } // mpileup - if (conf->vcf) ma = mc_init(n); + if (conf->flag & MPLP_GLF) { + bca = bcf_call_init(-1., conf->min_baseQ); + bcr = calloc(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) { @@ -548,55 +575,18 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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); -// printf("%lg->%lg\n", flast, f); - if (fabs(f - flast) < 1e-3) break; - flast = f; - } - if (1. - f < 1e-4) f = 1.; - 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'); + 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, bh, b); + //fprintf(stderr, "%d,%d,%d\n", b->tid, b->pos, b->l_str); + 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) { @@ -618,13 +608,14 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) putchar('\n'); } } + bcf_close(bp); 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); + 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) { @@ -642,18 +633,22 @@ int bam_mpileup(int argc, char *argv[]) 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) { + mplp.theta = 1e-3; + mplp.min_baseQ = 13; + while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:u")) >= 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); 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 '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 (argc == 1) { @@ -663,11 +658,12 @@ 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 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, " -V generate VCF output (SNP calling)\n"); - fprintf(stderr, " -v show variant sites only\n"); + fprintf(stderr, " -t FLOAT scaled mutation rate [%lg]\n", mplp.theta); + fprintf(stderr, " -g generate GLF 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);