X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=80799e3b28af95208796424c31a4bf5b7dd24ba0;hb=63af098c78ef4163356c281e87bfb467adc8824d;hp=aef10d38e37797bd24e728e3dd13955e92dc7b64;hpb=6dc53c5ab2964e68e8936850d2339d047d2433ef;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index aef10d3..80799e3 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -5,7 +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" @@ -450,16 +449,11 @@ int bam_pileup(int argc, char *argv[]) * mpileup * ***********/ -#define MPLP_VCF 0x1 -#define MPLP_VAR 0x2 -#define MPLP_AFALL 0x8 #define MPLP_GLF 0x10 #define MPLP_NO_COMP 0x20 -#define MPLP_AFS_BLOCK 0x10000 - typedef struct { - int max_mq, min_mq, prior_type, flag, min_baseQ; + int max_mq, min_mq, flag, min_baseQ; double theta; char *reg, *fn_pos; faidx_t *fai; @@ -489,12 +483,9 @@ 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; @@ -564,33 +555,11 @@ 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); } ref_tid = -1; ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); @@ -618,57 +587,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) 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) { @@ -691,7 +609,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) } } bcf_close(bp); - if (conf->flag&MPLP_VCF) mc_dump_afs(ma); if (hash) { // free the hash table khint_t k; for (k = kh_begin(hash); k < kh_end(hash); ++k) @@ -699,7 +616,6 @@ 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 +633,11 @@ 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) { + while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:u")) >= 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 +645,12 @@ 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 '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 +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, " -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, "\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);