X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=dca85181f99bf1c7343650846039153a019e7ea9;hb=3bedbd7fb801e7d0ffdedf2eb53dcce9ff08d31a;hp=358e9f99daea56c43dec513f82e64dacc13bd843;hpb=9e59c3bca7bf72427f3d5934ba56c3fe1cbd8285;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index 358e9f9..dca8518 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -22,6 +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; @@ -32,6 +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 @@ -89,6 +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) { @@ -158,29 +175,38 @@ 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) +static inline 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); + int j; + 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'; - if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.'; - else c = bam1_strand(p->b)? tolower(c) : toupper(c); + int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; + if (ref) { + int rb = pos < ref_len? ref[pos] : 'N'; + if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.'; + else c = bam1_strand(p->b)? tolower(c) : toupper(c); + } else { + if (c == '=') 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(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*'); + if (p->indel > 0) { + putchar('+'); printw(p->indel, stdout); + for (j = 1; j <= p->indel; ++j) { + int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)]; + putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); } - } else putchar('*'); + } else if (p->indel < 0) { + printw(p->indel, stdout); + for (j = 1; j <= -p->indel; ++j) { + int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N'; + putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); + } + } if (p->is_tail) putchar('$'); } @@ -232,7 +258,11 @@ 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; @@ -242,7 +272,7 @@ 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; @@ -250,30 +280,29 @@ 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); - 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; - 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); - } + printw(n, stdout); putchar('\t'); + for (i = 0; i < n; ++i) + pileup_seq(pu + i, 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; + 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) { @@ -312,7 +341,7 @@ 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'); @@ -338,13 +367,15 @@ 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; @@ -383,23 +414,26 @@ int bam_pileup(int argc, char *argv[]) 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 +461,43 @@ 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; + 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 } @@ -461,7 +531,6 @@ int bam_pileup(int argc, char *argv[]) typedef struct { int max_mq, min_mq, flag, min_baseQ, capQ_thres; - double theta; char *reg, *fn_pos; faidx_t *fai; kh_64_t *hash; @@ -483,6 +552,7 @@ typedef struct { 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, skip = 0; @@ -491,7 +561,7 @@ static int mplp_func(void *data, bam1_t *b) ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); if (ret < 0) break; skip = 0; - if (has_ref && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref); + 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; @@ -697,12 +767,11 @@ int bam_mpileup(int argc, char *argv[]) mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.max_mq = 60; - mplp.theta = 1e-3; mplp.min_baseQ = 13; mplp.capQ_thres = 0; - while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC:")) >= 0) { + mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN; + while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) { switch (c) { - case 't': mplp.theta = atof(optarg); break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == 0) return 1; @@ -710,8 +779,9 @@ 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 '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 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break; case 'O': mplp.flag |= MPLP_NO_ORPHAN; break; case 'R': mplp.flag |= MPLP_REALN; break; case 'C': mplp.capQ_thres = atoi(optarg); break; @@ -729,9 +799,9 @@ int bam_mpileup(int argc, char *argv[]) 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, " -g generate BCF output\n"); fprintf(stderr, " -u do not compress BCF output\n"); + fprintf(stderr, " -B disable BAQ computation\n"); fprintf(stderr, "\n"); fprintf(stderr, "Notes: Assuming diploid individuals.\n\n"); return 1;