static int mplp_func(void *data, bam1_t *b) { extern int bam_realn(bam1_t *b, const char *ref); extern int bam_prob_realn_core(bam1_t *b, const char *ref, int ref_len, int flag); extern int bam_cap_mapQ(bam1_t *b, char *ref, int ref_len, int thres); char *ref; mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0, ref_len; do { int has_ref; ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b); if (ret < 0) break; // The 'B' cigar operation is not part of the specification, considering as obsolete. // bam_remove_B(b); if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads skip = 1; continue; } if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; } if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; } if (ma->conf->bed) { // test overlap skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_endpos(b)); if (skip) continue; } if (ma->conf->rghash) { // exclude read groups uint8_t *rg = bam_aux_get(b, "RG"); skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0); if (skip) continue; } if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam_get_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } if (ma->conf->fai && b->core.tid >= 0) { has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len); if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n", __func__, b->core.pos, ref_len, b->core.tid); skip = 1; continue; } } else { has_ref = 0; } skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { int q = bam_cap_mapQ(b, ref, ref_len, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } if (b->core.qual < ma->conf->min_mq) skip = 1; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1; } while (skip); return ret; }
int main(int argc, char **argv) { dlib::BamHandle in = dlib::BamHandle("bed_test.bam"); dlib::ParsedBed bed = dlib::ParsedBed("bed_test.bed", in.header); bam1_t *b = bam_init1(); size_t diffs = 0; void *lh3bed = bed_read("bed_test.bed"); samFile *so = sam_open("disagreed.bam", "wb9"); sam_hdr_write(so, in.header); size_t disagrees = 0, agrees = 0; int dbr = 0, lh3r = 0; while(in.read(b) != -1) { if(b->core.flag & (BAM_FUNMAP)) continue; if((dbr = bed.bam1_test(b)) != (lh3r = bed_overlap(lh3bed, in.header->target_name[b->core.tid], b->core.pos, bam_endpos(b)))) { LOG_EXIT("dbr: %i. lh3r: %i. Contig: %s. Position: %i. endpos; %i\n", dbr, lh3r, in.header->target_name[b->core.tid], b->core.pos, bam_endpos(b)); if(++disagrees % 100 == 0) LOG_DEBUG("disagrees: %lu.\n", disagrees); sam_write1(so, in.header, b); } else { if(++agrees % 500000 == 0) LOG_DEBUG("agrees: %lu.\n", agrees); } } sam_close(so); bam_destroy1(b); bed_destroy(lh3bed); return EXIT_SUCCESS; }
static int mplp_func(void *data, bam1_t *b) { extern int bam_realn(bam1_t *b, const char *ref); extern int bam_prob_realn_core(bam1_t *b, const char *ref, int); extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0; do { int has_ref; ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); if (ret < 0) break; if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads skip = 1; continue; } if (ma->conf->bed) { // test overlap skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))); if (skip) continue; } if (ma->conf->rghash) { // exclude read groups uint8_t *rg = bam_aux_get(b, "RG"); skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0); if (skip) continue; } if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam1_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1); if (has_ref && ma->conf->capQ_thres > 10) { int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } else if (b->core.qual < ma->conf->min_mq) skip = 1; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; } while (skip); return ret; }
// Returns 0 to indicate read should be output 1 otherwise static int process_aln(const bam_hdr_t *h, bam1_t *b, samview_settings_t* settings) { if (settings->remove_B) bam_remove_B(b); if (settings->min_qlen > 0) { int k, qlen = 0; uint32_t *cigar = bam_get_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP) qlen += bam_cigar_oplen(cigar[k]); if (qlen < settings->min_qlen) return 1; } if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off)) return 1; if (settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, h->target_name[b->core.tid], b->core.pos, bam_endpos(b)))) return 1; if (settings->subsam_frac > 0.) { uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed); if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1; } if (settings->rghash) { uint8_t *s = bam_aux_get(b, "RG"); if (s) { khint_t k = kh_get(rg, settings->rghash, (char*)(s + 1)); if (k == kh_end(settings->rghash)) return 1; } } if (settings->library) { const char *p = bam_get_library((bam_hdr_t*)h, b); if (!p || strcmp(p, settings->library) != 0) return 1; } if (settings->remove_aux_len) { size_t i; for (i = 0; i < settings->remove_aux_len; ++i) { uint8_t *s = bam_aux_get(b, settings->remove_aux[i]); if (s) { bam_aux_del(b, s); } } } return 0; }
static int mpileup(mplp_conf_t *conf, int n, char **fn) { extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list); extern void bcf_call_del_rghash(void *rghash); mplp_aux_t **data; int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; const bam_pileup1_t **plp; bam_mplp_t iter; bam_header_t *h = 0; char *ref; void *rghash = 0; bcf_callaux_t *bca = 0; bcf_callret1_t *bcr = 0; bcf_call_t bc; bcf_t *bp = 0; bcf_hdr_t *bh = 0; bam_sample_t *sm = 0; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); memset(&bc, 0, sizeof(bcf_call_t)); data = calloc(n, sizeof(void*)); plp = calloc(n, sizeof(void*)); n_plp = calloc(n, sizeof(int*)); sm = bam_smpl_init(); // 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]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); data[i]->conf = conf; h_tmp = bam_header_read(data[i]->fp); data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text); rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list); 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) tid0 = tid, 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); } } gplp.n = sm->n; gplp.n_plp = calloc(sm->n, sizeof(int)); gplp.m_plp = calloc(sm->n, sizeof(int)); gplp.plp = calloc(sm->n, sizeof(void*)); fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n); // write the VCF header if (conf->flag & MPLP_GLF) { kstring_t s; bh = calloc(1, sizeof(bcf_hdr_t)); s.l = s.m = 0; s.s = 0; 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 < sm->n; ++i) { kputs(sm->smpl[i], &s); kputc('\0', &s); } bh->l_smpl = s.l; bh->sname = malloc(s.l); memcpy(bh->sname, s.s, s.l); bh->txt = malloc(strlen(BAM_VERSION) + 64); bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION); free(s.s); bcf_hdr_sync(bh); bcf_hdr_write(bp, bh); bca = bcf_call_init(-1., conf->min_baseQ); bcr = calloc(sm->n, sizeof(bcf_callret1_t)); bca->rghash = rghash; bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; bca->min_frac = conf->min_frac; bca->min_support = conf->min_support; } if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; } else ref_tid = -1, ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); max_depth = conf->max_depth; if (max_depth * sm->n > 1<<20) fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__); if (max_depth * sm->n < 8000) { max_depth = 8000 / sm->n; fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth); } max_indel_depth = conf->max_indel_depth * sm->n; bam_mplp_set_maxcnt(iter, max_depth); 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 (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue; if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } if (conf->flag & MPLP_GLF) { int total_depth, _ref0, ref16; bcf1_t *b = calloc(1, sizeof(bcf1_t)); for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i]; group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = bam_nt16_table[_ref0]; for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); bcf_call_combine(gplp.n, bcr, ref16, &bc); bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP), 0, 0); bcf_write(bp, bh, b); bcf_destroy(b); // call indels if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) { for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) { b = calloc(1, sizeof(bcf1_t)); bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP), bca, ref); bcf_write(bp, bh, b); 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) { int j; printf("\t%d\t", n_plp[i]); if (n_plp[i] == 0) { printf("*\t*"); // FIXME: printf() is very slow... if (conf->flag & MPLP_PRINT_POS) 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); } if (conf->flag & MPLP_PRINT_MAPQ) { putchar('\t'); for (j = 0; j < n_plp[i]; ++j) { int c = plp[i][j].b->core.qual + 33; if (c > 126) c = 126; putchar(c); } } if (conf->flag & MPLP_PRINT_POS) { putchar('\t'); for (j = 0; j < n_plp[i]; ++j) { if (j > 0) putchar(','); printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow... } } } } putchar('\n'); } } bcf_close(bp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bcf_call_del_rghash(rghash); 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) { 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 main(int argc, char *argv[]) { int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, bed_reg = 0; ti_conf_t conf = ti_conf_gff; const char *reheader = NULL; while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhfBr:")) >= 0) { switch (c) { case 'B': bed_reg = 1; break; case '0': conf.preset |= TI_FLAG_UCSC; break; case 'S': skip = atoi(optarg); break; case 'c': meta = optarg[0]; break; case 'p': if (strcmp(optarg, "gff") == 0) conf = ti_conf_gff; else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed; else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam; else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf = ti_conf_vcf; else if (strcmp(optarg, "psltbl") == 0) conf = ti_conf_psltbl; else { fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg); return 1; } break; case 's': conf.sc = atoi(optarg); break; case 'b': conf.bc = atoi(optarg); break; case 'e': conf.ec = atoi(optarg); break; case 'l': list_chrms = 1; break; case 'h': print_header = 1; break; case 'f': force = 1; break; case 'r': reheader = optarg; break; } } if (skip >= 0) conf.line_skip = skip; if (meta >= 0) conf.meta_char = meta; if (optind == argc) { fprintf(stderr, "\n"); fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n"); fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION); fprintf(stderr, "Usage: tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n"); fprintf(stderr, "Options: -p STR preset: gff, bed, sam, vcf, psltbl [gff]\n"); fprintf(stderr, " -s INT sequence name column [1]\n"); fprintf(stderr, " -b INT start column [4]\n"); fprintf(stderr, " -e INT end column; can be identical to '-b' [5]\n"); fprintf(stderr, " -S INT skip first INT lines [0]\n"); fprintf(stderr, " -c CHAR symbol for comment/meta lines [#]\n"); fprintf(stderr, " -r FILE replace the header with the content of FILE [null]\n"); fprintf(stderr, " -B region1 is a BED file (entire file will be read)\n"); fprintf(stderr, " -0 zero-based coordinate\n"); fprintf(stderr, " -h print the header lines\n"); fprintf(stderr, " -l list chromosome names\n"); fprintf(stderr, " -f force to overwrite the index\n"); fprintf(stderr, "\n"); return 1; } if (list_chrms) { ti_index_t *idx; int i, n; const char **names; idx = ti_index_load(argv[optind]); if (idx == 0) { fprintf(stderr, "[main] fail to load the index file.\n"); return 1; } names = ti_seqname(idx, &n); for (i = 0; i < n; ++i) printf("%s\n", names[i]); free(names); ti_index_destroy(idx); return 0; } if (reheader) return reheader_file(reheader,argv[optind],conf.meta_char); struct stat stat_tbi,stat_vcf; char *fnidx = calloc(strlen(argv[optind]) + 5, 1); strcat(strcpy(fnidx, argv[optind]), ".tbi"); if (optind + 1 == argc) { if (force == 0) { if (stat(fnidx, &stat_tbi) == 0) { // Before complaining, check if the VCF file isn't newer. This is a common source of errors, // people tend not to notice that tabix failed stat(argv[optind], &stat_vcf); if ( stat_vcf.st_mtime <= stat_tbi.st_mtime ) { fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n"); free(fnidx); return 1; } } } if ( bgzf_check_bgzf(argv[optind])!=1 ) { fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]); free(fnidx); return 1; } return ti_index_build(argv[optind], &conf); } { // retrieve tabix_t *t; // Common source of errors: new VCF is used with an old index stat(fnidx, &stat_tbi); stat(argv[optind], &stat_vcf); if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime ) { fprintf(stderr, "[tabix] the index file is older than the vcf file. Please use '-f' to overwrite or reindex.\n"); free(fnidx); return 1; } free(fnidx); if ((t = ti_open(argv[optind], 0)) == 0) { fprintf(stderr, "[main] fail to open the data file.\n"); return 1; } if (strcmp(argv[optind+1], ".") == 0) { // retrieve all ti_iter_t iter; const char *s; int len; iter = ti_query(t, 0, 0, 0); while ((s = ti_read(t, iter, &len)) != 0) { fputs(s, stdout); fputc('\n', stdout); } ti_iter_destroy(iter); } else { // retrieve from specified regions int i, len; ti_iter_t iter; const char *s; const ti_conf_t *idxconf; if (ti_lazy_index_load(t) < 0 && bed_reg == 0) { fprintf(stderr,"[tabix] failed to load the index file.\n"); return 1; } idxconf = ti_get_conf(t->idx); if ( print_header ) { // If requested, print the header lines here iter = ti_query(t, 0, 0, 0); while ((s = ti_read(t, iter, &len)) != 0) { if ((int)(*s) != idxconf->meta_char) break; fputs(s, stdout); fputc('\n', stdout); } ti_iter_destroy(iter); } if (bed_reg) { extern int bed_overlap(const void *_h, const char *chr, int beg, int end); extern void *bed_read(const char *fn); extern void bed_destroy(void *_h); const ti_conf_t *conf_ = idxconf? idxconf : &conf; // use the index file if available void *bed = bed_read(argv[optind+1]); // load the BED file ti_interval_t intv; if (bed == 0) { fprintf(stderr, "[main] fail to read the BED file.\n"); return 1; } iter = ti_query(t, 0, 0, 0); while ((s = ti_read(t, iter, &len)) != 0) { int c; ti_get_intv(conf_, len, (char*)s, &intv); c = *intv.se; *intv.se = '\0'; if (bed_overlap(bed, intv.ss, intv.beg, intv.end)) { *intv.se = c; puts(s); } *intv.se = c; } ti_iter_destroy(iter); bed_destroy(bed); } else { for (i = optind + 1; i < argc; ++i) { int tid, beg, end; if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) { iter = ti_queryi(t, tid, beg, end); while ((s = ti_read(t, iter, &len)) != 0) { fputs(s, stdout); fputc('\n', stdout); } ti_iter_destroy(iter); } // else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n"); } } } ti_close(t); } return 0; }
int main_depth(int argc, char *argv[]) #endif { int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0; const bam_pileup1_t **plp; char *reg = 0; // specified region void *bed = 0; // BED data structure bam_header_t *h = 0; // BAM header of the 1st input aux_t **data; bam_mplp_t mplp; // parse the command line while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) { switch (n) { case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now case 'q': baseQ = atoi(optarg); break; // base quality threshold case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold } } if (optind == argc) { fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed] <in1.bam> [...]\n"); return 1; } // initialize the auxiliary data structures n = argc - optind; // the number of BAMs on the command line data = (aux_t **) calloc(n, sizeof(void*)); // data[i] for the i-th input beg = 0; end = 1<<30; tid = -1; // set the default region for (i = 0; i < n; ++i) { bam_header_t *htmp; data[i] = (aux_t *) calloc(1, sizeof(aux_t)); data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM data[i]->min_mapQ = mapQ; // set the mapQ filter htmp = bam_header_read(data[i]->fp); // read the BAM header if (i == 0) { h = htmp; // keep the header of the 1st BAM if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header if (tid >= 0) { // if a region is specified and parsed successfully bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator bam_index_destroy(idx); // the index is not needed any more; phase out of the memory } } // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization n_plp = (int*) calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = (bam_pileup1_t **) calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position if (pos < beg || pos >= end) continue; // out of range; skip if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster for (i = 0; i < n; ++i) { // base level filters have to go here int j, m = 0; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality } printf("\t%d", n_plp[i] - m); // this the depth to output } putchar('\n'); } free(n_plp); free(plp); bam_mplp_destroy(mplp); 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(reg); if (bed) bed_destroy(bed); return 0; }
int main_depth(int argc, char *argv[]) { int i, n, tid, reg_tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0; int all = 0, status = EXIT_SUCCESS, nfiles, max_depth = -1; const bam_pileup1_t **plp; char *reg = 0; // specified region void *bed = 0; // BED data structure char *file_list = NULL, **fn = NULL; bam_hdr_t *h = NULL; // BAM header of the 1st input aux_t **data; bam_mplp_t mplp; int last_pos = -1, last_tid = -1, ret; sam_global_args ga = SAM_GLOBAL_ARGS_INIT; static const struct option lopts[] = { SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0), { NULL, 0, NULL, 0 } }; // parse the command line while ((n = getopt_long(argc, argv, "r:b:q:Q:l:f:am:d:", lopts, NULL)) >= 0) { switch (n) { case 'l': min_len = atoi(optarg); break; // minimum query length case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header case 'b': bed = bed_read(optarg); // BED or position list file can be parsed now if (!bed) { print_error_errno("depth", "Could not read file \"%s\"", optarg); return 1; } break; case 'q': baseQ = atoi(optarg); break; // base quality threshold case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold case 'f': file_list = optarg; break; case 'a': all++; break; case 'd': case 'm': max_depth = atoi(optarg); break; // maximum coverage depth default: if (parse_sam_global_opt(n, optarg, lopts, &ga) == 0) break; /* else fall-through */ case '?': return usage(); } } if (optind == argc && !file_list) return usage(); // initialize the auxiliary data structures if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) return 1; n = nfiles; argv = fn; optind = 0; } else n = argc - optind; // the number of BAMs on the command line data = calloc(n, sizeof(aux_t*)); // data[i] for the i-th input reg_tid = 0; beg = 0; end = INT_MAX; // set the default region for (i = 0; i < n; ++i) { int rf; data[i] = calloc(1, sizeof(aux_t)); data[i]->fp = sam_open_format(argv[optind+i], "r", &ga.in); // open BAM if (data[i]->fp == NULL) { print_error_errno("depth", "Could not open \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto depth_end; } rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; if (baseQ) rf |= SAM_QUAL; if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) { fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } data[i]->min_mapQ = mapQ; // set the mapQ filter data[i]->min_len = min_len; // set the qlen filter data[i]->hdr = sam_hdr_read(data[i]->fp); // read the BAM header if (data[i]->hdr == NULL) { fprintf(stderr, "Couldn't read header for \"%s\"\n", argv[optind+i]); status = EXIT_FAILURE; goto depth_end; } if (reg) { // if a region is specified hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]); // load the index if (idx == NULL) { print_error("depth", "can't load index for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto depth_end; } data[i]->iter = sam_itr_querys(idx, data[i]->hdr, reg); // set the iterator hts_idx_destroy(idx); // the index is not needed any more; free the memory if (data[i]->iter == NULL) { print_error("depth", "can't parse region \"%s\"", reg); status = EXIT_FAILURE; goto depth_end; } } } h = data[0]->hdr; // easy access to the header of the 1st BAM if (reg) { beg = data[0]->iter->beg; // and to the parsed region coordinates end = data[0]->iter->end; reg_tid = data[0]->iter->tid; } // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization if (0 < max_depth) bam_mplp_set_maxcnt(mplp,max_depth); // set maximum coverage depth n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp) while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position if (pos < beg || pos >= end) continue; // out of range; skip if (tid >= h->n_targets) continue; // diff number of @SQ lines per file? if (all) { while (tid > last_tid) { if (last_tid >= 0 && !reg) { // Deal with remainder or entirety of last tid. while (++last_pos < h->target_len[last_tid]) { // Horribly inefficient, but the bed API is an obfuscated black box. if (bed && bed_overlap(bed, h->target_name[last_tid], last_pos, last_pos + 1) == 0) continue; fputs(h->target_name[last_tid], stdout); printf("\t%d", last_pos+1); for (i = 0; i < n; i++) putchar('\t'), putchar('0'); putchar('\n'); } } last_tid++; last_pos = -1; if (all < 2) break; } // Deal with missing portion of current tid while (++last_pos < pos) { if (last_pos < beg) continue; // out of range; skip if (bed && bed_overlap(bed, h->target_name[tid], last_pos, last_pos + 1) == 0) continue; fputs(h->target_name[tid], stdout); printf("\t%d", last_pos+1); for (i = 0; i < n; i++) putchar('\t'), putchar('0'); putchar('\n'); } last_tid = tid; last_pos = pos; } if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster for (i = 0; i < n; ++i) { // base level filters have to go here int j, m = 0; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos else if (bam_get_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality } printf("\t%d", n_plp[i] - m); // this the depth to output } putchar('\n'); } if (ret < 0) status = EXIT_FAILURE; free(n_plp); free(plp); bam_mplp_destroy(mplp); if (all) { // Handle terminating region if (last_tid < 0 && reg && all > 1) { last_tid = reg_tid; last_pos = beg-1; } while (last_tid >= 0 && last_tid < h->n_targets) { while (++last_pos < h->target_len[last_tid]) { if (last_pos >= end) break; if (bed && bed_overlap(bed, h->target_name[last_tid], last_pos, last_pos + 1) == 0) continue; fputs(h->target_name[last_tid], stdout); printf("\t%d", last_pos+1); for (i = 0; i < n; i++) putchar('\t'), putchar('0'); putchar('\n'); } last_tid++; last_pos = -1; if (all < 2 || reg) break; } } depth_end: for (i = 0; i < n && data[i]; ++i) { bam_hdr_destroy(data[i]->hdr); if (data[i]->fp) sam_close(data[i]->fp); hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); free(reg); if (bed) bed_destroy(bed); if ( file_list ) { for (i=0; i<n; i++) free(fn[i]); free(fn); } sam_global_args_free(&ga); return status; }
int main_depth(int argc, char *argv[]) #endif { int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles; const bam_pileup1_t **plp; char *reg = 0; // specified region void *bed = 0; // BED data structure char *file_list = NULL, **fn = NULL; bam_header_t *h = 0; // BAM header of the 1st input aux_t **data; bam_mplp_t mplp; // parse the command line while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) { switch (n) { case 'l': min_len = atoi(optarg); break; // minimum query length case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now case 'q': baseQ = atoi(optarg); break; // base quality threshold case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold case 'f': file_list = optarg; break; } } if (optind == argc && !file_list) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -b <bed> list of positions or regions\n"); fprintf(stderr, " -f <list> list of input BAM filenames, one per line [null]\n"); fprintf(stderr, " -l <int> minQLen\n"); fprintf(stderr, " -q <int> base quality threshold\n"); fprintf(stderr, " -Q <int> mapping quality threshold\n"); fprintf(stderr, " -r <chr:from-to> region\n"); fprintf(stderr, "\n"); return 1; } // initialize the auxiliary data structures if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) return 1; n = nfiles; argv = fn; optind = 0; } else n = argc - optind; // the number of BAMs on the command line data = calloc(n, sizeof(void*)); // data[i] for the i-th input beg = 0; end = 1<<30; tid = -1; // set the default region for (i = 0; i < n; ++i) { bam_header_t *htmp; data[i] = calloc(1, sizeof(aux_t)); data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM data[i]->min_mapQ = mapQ; // set the mapQ filter data[i]->min_len = min_len; // set the qlen filter htmp = bam_header_read(data[i]->fp); // read the BAM header if (i == 0) { h = htmp; // keep the header of the 1st BAM if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header if (tid >= 0) { // if a region is specified and parsed successfully bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator bam_index_destroy(idx); // the index is not needed any more; phase out of the memory } } // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization bam_mplp_set_maxcnt(mplp,2147483647); // set max_depth to int max n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position if (pos < beg || pos >= end) continue; // out of range; skip if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster for (i = 0; i < n; ++i) { // base level filters have to go here int j, m = 0; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality } printf("\t%d", n_plp[i] - m); // this the depth to output } putchar('\n'); } free(n_plp); free(plp); bam_mplp_destroy(mplp); 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(reg); if (bed) bed_destroy(bed); if ( file_list ) { for (i=0; i<n; i++) free(fn[i]); free(fn); } return 0; }
/* * Performs pileup * @param conf configuration for this pileup * @param n number of files specified in fn * @param fn filenames */ static int mpileup(mplp_conf_t *conf, int n, char **fn) { extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list); extern void bcf_call_del_rghash(void *rghash); mplp_aux_t **data; int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; const bam_pileup1_t **plp; bam_mplp_t iter; bam_hdr_t *h = NULL; /* header of first file in input list */ char *ref; void *rghash = NULL; FILE *pileup_fp = NULL; bcf_callaux_t *bca = NULL; bcf_callret1_t *bcr = NULL; bcf_call_t bc; htsFile *bcf_fp = NULL; bcf_hdr_t *bcf_hdr = NULL; bam_sample_t *sm = NULL; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); memset(&bc, 0, sizeof(bcf_call_t)); data = calloc(n, sizeof(mplp_aux_t*)); plp = calloc(n, sizeof(bam_pileup1_t*)); n_plp = calloc(n, sizeof(int)); sm = bam_smpl_init(); if (n == 0) { fprintf(stderr,"[%s] no input file/data given\n", __func__); exit(1); } // read the header of each file in the list and initialize data for (i = 0; i < n; ++i) { bam_hdr_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); data[i]->fp = sam_open(fn[i], "rb"); if ( !data[i]->fp ) { fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno)); exit(1); } hts_set_fai_filename(data[i]->fp, conf->fai_fname); data[i]->conf = conf; h_tmp = sam_hdr_read(data[i]->fp); if ( !h_tmp ) { fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]); exit(1); } data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text); // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search) rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list); if (conf->reg) { hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]); if (idx == 0) { fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]); exit(1); } if ( (data[i]->iter=sam_itr_querys(idx, data[i]->h, conf->reg)) == 0) { fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, conf->reg); exit(1); } if (i == 0) tid0 = data[i]->iter->tid, beg0 = data[i]->iter->beg, end0 = data[i]->iter->end; hts_idx_destroy(idx); } if (i == 0) h = h_tmp; /* save the header of first file in list */ else { // FIXME: to check consistency bam_hdr_destroy(h_tmp); } } // allocate data storage proportionate to number of samples being studied sm->n gplp.n = sm->n; gplp.n_plp = calloc(sm->n, sizeof(int)); gplp.m_plp = calloc(sm->n, sizeof(int)); gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*)); fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n); // write the VCF header if (conf->flag & MPLP_BCF) { const char *mode; if ( conf->flag & MPLP_VCF ) mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz"; // uncompressed VCF or compressed VCF else mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb"; // uncompressed BCF or compressed BCF bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode); if (bcf_fp == NULL) { fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno)); exit(1); } bcf_hdr = bcf_hdr_init("w"); kstring_t str = {0,0,0}; ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version()); bcf_hdr_append(bcf_hdr, str.s); str.l = 0; ksprintf(&str, "##samtoolsCommand=samtools mpileup"); for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]); kputc('\n', &str); bcf_hdr_append(bcf_hdr, str.s); if (conf->fai_fname) { str.l = 0; ksprintf(&str, "##reference=file://%s\n", conf->fai_fname); bcf_hdr_append(bcf_hdr, str.s); } // todo: use/write new BAM header manipulation routines, fill also UR, M5 for (i=0; i<h->n_targets; i++) { str.l = 0; ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]); bcf_hdr_append(bcf_hdr, str.s); } free(str.s); bcf_hdr_append(bcf_hdr,"##ALT=<ID=X,Description=\"Represents allele(s) other than observed.\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">"); #if CDF_MWU_TESTS bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">"); #endif bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">"); bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">"); bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">"); if ( conf->fmt_flag&B2B_FMT_DP ) bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">"); if ( conf->fmt_flag&B2B_FMT_DV ) bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">"); if ( conf->fmt_flag&B2B_FMT_DPR ) bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">"); if ( conf->fmt_flag&B2B_INFO_DPR ) bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">"); if ( conf->fmt_flag&B2B_FMT_DP4 ) bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">"); if ( conf->fmt_flag&B2B_FMT_SP ) bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">"); for (i=0; i<sm->n; i++) bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]); bcf_hdr_add_sample(bcf_hdr, NULL); bcf_hdr_write(bcf_fp, bcf_hdr); bca = bcf_call_init(-1., conf->min_baseQ); bcr = calloc(sm->n, sizeof(bcf_callret1_t)); bca->rghash = rghash; bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; bca->min_frac = conf->min_frac; bca->min_support = conf->min_support; bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE; bc.bcf_hdr = bcf_hdr; bc.n = sm->n; bc.PL = malloc(15 * sm->n * sizeof(*bc.PL)); if (conf->fmt_flag) { assert( sizeof(float)==sizeof(int32_t) ); bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4); bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR) ) { // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample bc.DPR = malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t)); for (i=0; i<sm->n; i++) bcr[i].DPR = bc.DPR + (i+1)*B2B_MAX_ALLELES; } } } else { pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout; if (pileup_fp == NULL) { fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno)); exit(1); } } if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; } else ref_tid = -1, ref = 0; // begin pileup iter = bam_mplp_init(n, mplp_func, (void**)data); if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter); max_depth = conf->max_depth; if (max_depth * sm->n > 1<<20) fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__); if (max_depth * sm->n < 8000) { max_depth = 8000 / sm->n; fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth); } max_indel_depth = conf->max_indel_depth * sm->n; bam_mplp_set_maxcnt(iter, max_depth); bcf1_t *bcf_rec = bcf_init1(); int ret; while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) { if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue; if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } if (conf->flag & MPLP_BCF) { int total_depth, _ref0, ref16; for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i]; group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = seq_nt16_table[_ref0]; bcf_callaux_clean(bca, &bc); for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); bc.tid = tid; bc.pos = pos; bcf_call_combine(gplp.n, bcr, bca, ref16, &bc); bcf_clear1(bcf_rec); bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0); bcf_write1(bcf_fp, bcf_hdr, bcf_rec); // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring? if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) { bcf_callaux_clean(bca, &bc); for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) { bcf_clear1(bcf_rec); bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref); bcf_write1(bcf_fp, bcf_hdr, bcf_rec); } } } else { fprintf(pileup_fp, "%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, cnt; for (j = cnt = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; if (bam_get_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt; } fprintf(pileup_fp, "\t%d\t", cnt); if (n_plp[i] == 0) { fputs("*\t*", pileup_fp); if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", pileup_fp); if (conf->flag & MPLP_PRINT_POS) fputs("\t*", pileup_fp); } else { for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; if (bam_get_qual(p->b)[p->qpos] >= conf->min_baseQ) pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref); } putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; int c = bam_get_qual(p->b)[p->qpos]; if (c >= conf->min_baseQ) { c = c + 33 < 126? c + 33 : 126; putc(c, pileup_fp); } } if (conf->flag & MPLP_PRINT_MAPQ) { putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; int c = bam_get_qual(p->b)[p->qpos]; if ( c < conf->min_baseQ ) continue; c = plp[i][j].b->core.qual + 33; if (c > 126) c = 126; putc(c, pileup_fp); } } if (conf->flag & MPLP_PRINT_POS) { putc('\t', pileup_fp); for (j = 0; j < n_plp[i]; ++j) { if (j > 0) putc(',', pileup_fp); fprintf(pileup_fp, "%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow... } } } } putc('\n', pileup_fp); } } // clean up free(bc.tmp.s); bcf_destroy1(bcf_rec); if (bcf_fp) { hts_close(bcf_fp); bcf_hdr_destroy(bcf_hdr); bcf_call_destroy(bca); free(bc.PL); free(bc.DP4); free(bc.DPR); free(bc.fmt_arr); free(bcr); } if (pileup_fp && conf->output_fname) fclose(pileup_fp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bcf_call_del_rghash(rghash); bam_mplp_destroy(iter); bam_hdr_destroy(h); for (i = 0; i < n; ++i) { sam_close(data[i]->fp); if (data[i]->iter) hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); free(plp); free(ref); free(n_plp); return ret; }
int main_depth(int argc, char *argv[]) { int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, status = EXIT_SUCCESS, nfiles; const bam_pileup1_t **plp; char *reg = 0; // specified region void *bed = 0; // BED data structure char *file_list = NULL, **fn = NULL; bam_hdr_t *h = NULL; // BAM header of the 1st input aux_t **data; bam_mplp_t mplp; // parse the command line while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) { switch (n) { case 'l': min_len = atoi(optarg); break; // minimum query length case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header case 'b': bed = bed_read(optarg); // BED or position list file can be parsed now if (!bed) { print_error_errno("Could not read file \"%s\"", optarg); return 1; } break; case 'q': baseQ = atoi(optarg); break; // base quality threshold case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold case 'f': file_list = optarg; break; } } if (optind == argc && !file_list) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n"); fprintf(pysamerr, "Options:\n"); fprintf(pysamerr, " -b <bed> list of positions or regions\n"); fprintf(pysamerr, " -f <list> list of input BAM filenames, one per line [null]\n"); fprintf(pysamerr, " -l <int> read length threshold (ignore reads shorter than <int>)\n"); fprintf(pysamerr, " -q <int> base quality threshold\n"); fprintf(pysamerr, " -Q <int> mapping quality threshold\n"); fprintf(pysamerr, " -r <chr:from-to> region\n"); fprintf(pysamerr, "\n"); return 1; } // initialize the auxiliary data structures if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) return 1; n = nfiles; argv = fn; optind = 0; } else n = argc - optind; // the number of BAMs on the command line data = calloc(n, sizeof(aux_t*)); // data[i] for the i-th input beg = 0; end = 1<<30; // set the default region for (i = 0; i < n; ++i) { data[i] = calloc(1, sizeof(aux_t)); data[i]->fp = sam_open(argv[optind+i], "r"); // open BAM if (data[i]->fp == NULL) { print_error_errno("Could not open \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto depth_end; } if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ)) { fprintf(pysamerr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n"); return 1; } if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) { fprintf(pysamerr, "Failed to set CRAM_OPT_DECODE_MD value\n"); return 1; } data[i]->min_mapQ = mapQ; // set the mapQ filter data[i]->min_len = min_len; // set the qlen filter data[i]->hdr = sam_hdr_read(data[i]->fp); // read the BAM header if (reg) { // if a region is specified hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]); // load the index if (idx == NULL) { print_error("can't load index for \"%s\"", argv[optind+i]); status = EXIT_FAILURE; goto depth_end; } data[i]->iter = sam_itr_querys(idx, data[i]->hdr, reg); // set the iterator hts_idx_destroy(idx); // the index is not needed any more; free the memory if (data[i]->iter == NULL) { print_error("can't parse region \"%s\"", reg); status = EXIT_FAILURE; goto depth_end; } } } h = data[0]->hdr; // easy access to the header of the 1st BAM if (reg) { beg = data[0]->iter->beg; // and to the parsed region coordinates end = data[0]->iter->end; } // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position if (pos < beg || pos >= end) continue; // out of range; skip if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster for (i = 0; i < n; ++i) { // base level filters have to go here int j, m = 0; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos else if (bam_get_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality } printf("\t%d", n_plp[i] - m); // this the depth to output } putchar('\n'); } free(n_plp); free(plp); bam_mplp_destroy(mplp); depth_end: for (i = 0; i < n && data[i]; ++i) { bam_hdr_destroy(data[i]->hdr); if (data[i]->fp) sam_close(data[i]->fp); hts_itr_destroy(data[i]->iter); free(data[i]); } free(data); free(reg); if (bed) bed_destroy(bed); if ( file_list ) { for (i=0; i<n; i++) free(fn[i]); free(fn); } return status; }
static int mpileup(mplp_conf_t *conf, int n, char **fn) { extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list); extern void bcf_call_del_rghash(void *rghash); mplp_aux_t **data; int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; const bam_pileup1_t **plp; bam_mplp_t iter; bam_header_t *h = 0; char *ref; void *rghash = 0; bcf_callaux_t *bca = 0; bcf_callret1_t *bcr = 0; bcf_call_t bc; bcf_t *bp = 0; bcf_hdr_t *bh = 0; bam_sample_t *sm = 0; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); memset(&bc, 0, sizeof(bcf_call_t)); data = calloc(n, sizeof(void*)); plp = calloc(n, sizeof(void*)); n_plp = calloc(n, sizeof(int*)); sm = bam_smpl_init(); // 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]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); data[i]->conf = conf; h_tmp = bam_header_read(data[i]->fp); data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text); rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list); 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) tid0 = tid, 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); } } gplp.n = sm->n; gplp.n_plp = calloc(sm->n, sizeof(int)); gplp.m_plp = calloc(sm->n, sizeof(int)); gplp.plp = calloc(sm->n, sizeof(void*)); fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n); // write the VCF header if (conf->flag & MPLP_GLF) { kstring_t s; bh = calloc(1, sizeof(bcf_hdr_t)); s.l = s.m = 0; s.s = 0; 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 < sm->n; ++i) { kputs(sm->smpl[i], &s); kputc('\0', &s); } bh->l_smpl = s.l; bh->sname = malloc(s.l); memcpy(bh->sname, s.s, s.l); bh->txt = malloc(strlen(BAM_VERSION) + 64); bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION); free(s.s); bcf_hdr_sync(bh); bcf_hdr_write(bp, bh); bca = bcf_call_init(-1., conf->min_baseQ); bcr = calloc(sm->n, sizeof(bcf_callret1_t)); bca->rghash = rghash; bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; bca->min_frac = conf->min_frac; bca->min_support = conf->min_support; } if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; } else ref_tid = -1, ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); max_depth = conf->max_depth; if (max_depth * sm->n > 1<<20) fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__); if (max_depth * sm->n < 8000) { max_depth = 8000 / sm->n; fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth); } max_indel_depth = conf->max_indel_depth * sm->n; bam_mplp_set_maxcnt(iter, max_depth); int storeSize = 100; int delStore[2][100] = {{0},{0}}; typedef char * mstring; 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 (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue; if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } if (conf->flag & MPLP_GLF) { int total_depth, _ref0, ref16; bcf1_t *b = calloc(1, sizeof(bcf1_t)); for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i]; group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = bam_nt16_table[_ref0]; for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); bcf_call_combine(gplp.n, bcr, ref16, &bc); bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP), 0, 0); bcf_write(bp, bh, b); bcf_destroy(b); // call indels if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) { for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) { b = calloc(1, sizeof(bcf1_t)); bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP), bca, ref); bcf_write(bp, bh, b); 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) { int j; printf("\t%d\t", n_plp[i]); if (n_plp[i] == 0) { printf("*\t*"); // FIXME: printf() is very slow... if (conf->flag & MPLP_PRINT_POS) printf("\t*"); } else { //MDW start //for each position in the pileup column int charLen = 16; int countChars[ charLen ][2]; int countiChars[ charLen ][2]; int countGap[2]={0,0}; //double qvTotal=0; int numStruck=0; int numGood=0; int tti; int ttj; mstring insAllele[100]; int insAlleleCnt[100]; int sf=0; int flag=0; //typedef char * string; char insStr0[10000]; int iCnt0=0; char insStr1[10000]; int iCnt1=0; char delStr0[10000]; int dCnt0=0; char delStr1[10000]; int dCnt1=0; float qposP[10000]; int qposCnt=0; //initialize with zeros for(tti=0;tti<charLen;tti++){ countChars[tti][0]=0; countChars[tti][1]=0; } // define repeat length here; look back up to 10 prior positions // start one position away. int replC=0; // for(tti=1;tti<=15;tti++){ // check for greater than zero if(toupper(ref[pos-1])==toupper(ref[pos-tti])){ replC++; }else{ // breaks the chain at first non identical to current position not strict homopolymer break; } } int reprC=0; // for(tti=1;tti<=15;tti++){ // check for greater than zero if(toupper(ref[pos+1])==toupper(ref[pos+tti])){ reprC++; }else{ // breaks the chain at first non identical to current position not strict homopolymer break; } } int repT = replC; if(replC < reprC){ repT=reprC; } for (j = 0; j < n_plp[i]; ++j){ const bam_pileup1_t *p = plp[i] + j; /* SAME LOGIC AS pileup_seq() */ if(p->is_refskip){ // never count intron gaps in numStruck continue; } if(p->is_del){ // skip deletion gap, after first position which is the first aligned char continue; } if( p->b->core.qual < conf->min_mqToCount || // mapping quality conf->maxrepC < (repT) || // max homopolymer run, this will not (!p->is_del && bam1_qual(p->b)[p->qpos] < conf->min_baseQ) || // base quality for matches p->alignedQPosBeg <= (conf->trimEnd ) || p->alignedQPosEnd <= (conf->trimEnd ) || // trimEnd is 1-based p->zf == 1 || // fusion tag p->ih > conf->maxIH || // max hit index (p->nmd > conf->maxNM) || // max mismatch (conf->flagFilter == 1 && !(p->b->core.flag&BAM_FPROPER_PAIR)) || // optionally keep only proper pairs (conf->flagFilter == 2 && p->b->core.flag&BAM_FSECONDARY) || // optionally strike secondary (conf->flagFilter == 3 && p->b->core.flag&BAM_FDUP) || // optionally strike dup (conf->flagFilter == 4 && (p->b->core.flag&BAM_FDUP || p->b->core.flag&BAM_FSECONDARY)) || // optionally strike secondary or dup (conf->flagFilter == 5 && (p->b->core.flag&BAM_FDUP || p->b->core.flag&BAM_FSECONDARY || p->b->core.flag&BAM_FQCFAIL || !(p->b->core.flag&BAM_FPROPER_PAIR) )) // optionally strike secondary, dup and QCfail ){ numStruck++; continue; } //printf("repT=%d: %d %c %c %c %c \n",repT,p->indel,ref[pos],ref[pos-1],ref[pos-2],ref[pos-3]); if(!p->is_del && p->indel==0){ countChars[ bam1_seqi(bam1_seq(p->b), p->qpos) ][ bam1_strand(p->b) ] ++; numGood++; }else if(p->is_refskip){ countGap[ bam1_strand(p->b) ]++; } if(p->indel<0){ numGood++; if(bam1_strand(p->b) ==0){ for(tti=1;tti<= -p->indel; tti++) { // current spot, starting at 0 in store, because indel<0 refers to next position delStr0[dCnt0] = ref[pos+tti]; dCnt0++; } delStr0[dCnt0] = ','; dCnt0++; }else{ for(tti=1;tti<= -p->indel; tti++) { // current spot, starting at 0 in store, because indel<0 refers to next position delStr1[dCnt1] = ref[pos+tti]; dCnt1++; } delStr1[dCnt1] = ','; dCnt1++; } }else if(p->indel>0){ numGood++; if(bam1_strand(p->b) ==0){ for(tti=1;tti<= p->indel; tti++) { // current spot, starting at 0 in store, because indel<0 refers to next position insStr0[iCnt0] = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + tti)]; iCnt0++; } insStr0[iCnt0] = ','; iCnt0++; }else{ for(tti=1;tti<= p->indel; tti++) { // current spot, starting at 0 in store, because indel<0 refers to next position insStr1[iCnt1] = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + tti)]; iCnt1++; } insStr1[iCnt1] = ','; iCnt1++; } } //calculate position of variant within aligned read - no soft clips if( toupper(ref[pos]) != toupper(bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]) || p->indel>0 || p->indel<0 ){ //distance to end; calculate distance to end of aligned read. removes soft clips. int distToEnd = (p->alignedQPosBeg < p->alignedQPosEnd) ? p->alignedQPosBeg : p->alignedQPosEnd; qposP[qposCnt] = distToEnd; qposCnt++; // printf("id=%s, pos=%d",bam1_qname(p->b),distToEnd); } } // //print A,C,G,T, by +/- printf("\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d", countChars[1][0],countChars[1][1], countChars[2][0],countChars[2][1], countChars[4][0],countChars[4][1], countChars[8][0],countChars[8][1], countChars[7][0],countChars[7][1]); putchar('\t'); for(tti=0;tti<dCnt0;tti++){ putchar(delStr0[tti]); } putchar('\t'); for(tti=0;tti<dCnt1;tti++){ putchar(delStr1[tti]); } putchar('\t'); for(tti=0;tti<iCnt0;tti++){ putchar(insStr0[tti]); } putchar('\t'); for(tti=0;tti<iCnt1;tti++){ putchar(insStr1[tti]); } printf("\t%d\t%d",numGood,numStruck); // get non-ref qpos variation float medqpos = -1; float medAbsDev = -1; if(qposCnt>0){ medqpos = median(qposCnt,qposP); float absDev[qposCnt]; for(tti=0;tti<qposCnt;tti++){ absDev[tti] = abs(medqpos - qposP[tti]); } medAbsDev = median(qposCnt-1,absDev); } printf("\t%f",medAbsDev); ///END MDW } } putchar('\n'); } } bcf_close(bp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bcf_call_del_rghash(rghash); 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) { 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 main(int argc, char *argv[]) { int c, i, n, ret, res; int tid, pos, *n_plp; cmdopt_t o; bam_mplp_t mplp; const bam_pileup1_t **plp; aux_t **data; bam_hdr_t *h = 0; sv_t sv1; qual_sum_t qual2; khiter_t k_iter; khash_t(sv_hash) *sv_h = kh_init(sv_hash); khash_t(sv_geno) *geno_h = kh_init(sv_geno); khash_t(colmap) *smp_cols; khash_t(ped) *ped_h = 0; mempool_t *mp; char **samples; o.min_q = 40; o.min_s = 80; o.min_len = 150; o.min_dp = 10; o.bed = 0, o.fnped = 0, o.mi_prob=0.005; while ((c = getopt(argc, argv, "hq:s:l:d:b:p:m:")) >= 0) { if (c == 'h') { usage(stderr, &o); return 0; } else if (c == 'q') o.min_q = atoi(optarg); else if (c == 's') o.min_s = atoi(optarg); else if (c == 'l') o.min_len = atoi(optarg); else if (c == 'd') o.min_dp = atoi(optarg); else if (c == 'p') o.fnped = optarg; else if (c == 'm') o.mi_prob = atof(optarg); else if (c == 'b') { if ((o.bed = bed_read(optarg)) == NULL) { return -1; } } } if (o.mi_prob < 0.0000000000001 || o.mi_prob > 0.1) { fprintf(stderr, "Error. Probability of a mendelian inconsistency must be between 0.1 and 0.0000000000001.\n"); } if (argc - optind < 1) { usage(stderr, &o); return 1; } // Open files and initalize aux data // n = argc - optind; data = calloc(n, sizeof(aux_t*)); samples = (char**)malloc(n * sizeof(char*)); for (i = 0; i < n; ++i) { data[i] = calloc(1, sizeof (aux_t)); data[i]->fp = sam_open(argv[optind + i], "r"); if (!data[i]->fp) { fprintf(stderr, "Input file \"%s\" could not be opened.\n", argv[optind + 1]); return 1; } data[i]->min_mapq = o.min_q; data[i]->min_as = o.min_s; data[i]->min_len = o.min_len; data[i]->hdr = sam_hdr_read(data[i]->fp); if (!data[i]->hdr) { fprintf(stderr, "Could not read the header for input file \"%s\".\n", argv[optind + 1]); return 1; } samples[i] = find_sample(data[i]->hdr, &res); if (!samples[i]) { fprintf(stderr, "Warning. No sample name detected for bam %s. Using filename\n", argv[optind + i]); samples[i] = argv[optind + i]; } } h = data[0]->hdr; smp_cols = map_samples(samples, n); if (o.fnped) { if ((ped_h = read_ped(o.fnped, smp_cols)) == 0) { return -1; } } // The core data processing loop // mplp = bam_mplp_init(n, read_bam, (void**)data); n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads in mplp //quals = (qual_vec_t*)calloc(n, sizeof(qual_vec_t)); mp = mp_init(); while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // iterate of positions with coverage int n_sv; if (o.bed && tid >= 0 && !bed_overlap(o.bed, h->target_name[tid], pos, pos+1)) continue; n_sv = plp2sv(h, tid, pos, n, n_plp, plp, sv_h); if (n_sv > 1) { fprintf(stderr, "Warning: more than two alleles detected at %s:%d\n", h->target_name[tid], pos); } if (n_sv) { fprintf(stderr, "SV detected at %d:%d\n", tid, pos); for (k_iter = kh_begin(sv_h); k_iter != kh_end(sv_h); ++k_iter) { if (kh_exist(sv_h, k_iter)) { sv1 = kh_value(sv_h, k_iter); fprintf(stderr, "SV tid1=%d, tid2=%d, pos1=%d, pos2=%d, ori1=%d, ori2=%d, allele=%d\n", sv1.tid1, sv1.tid2, sv1.pos1, sv1.pos2, sv1.ori1, sv1.ori2, sv1.allele); } } res = get_qual_data(h, tid, pos, n, n_plp, plp, n_sv + 1, sv_h, geno_h, mp); if (res < 0) { fprintf(stderr, "Error collecting quality data from reads\n"); return -1; } kh_clear(sv_hash, sv_h); } } print_header(h, optind, n, argv); genotype_sv(h, n, geno_h, o.min_dp, ped_h, o.mi_prob); free(n_plp); free(plp); bam_mplp_destroy(mplp); mp_destroy(mp); if (o.bed) bed_destroy(o.bed); for (i = 0; i < n; ++i) { bam_hdr_destroy(data[i]->hdr); sam_close(data[i]->fp); free(data[i]); free(samples[i]); } free(data); free(samples); kh_destroy(sv_hash, sv_h); kh_destroy(sv_geno, geno_h); kh_destroy(colmap, smp_cols); kh_destroy(ped, ped_h); return 0; }