int main(int argc, char *argv[]) { char c; int opt_idx, node; FILE *out_f = NULL, *msa_f, *mod_f; char *out_root; TreeModel *mod; MSA *msa; char out_fname[STR_MED_LEN]; struct option long_opts[] = { {"refseq", 1, 0, 'r'}, {"msa-format", 1, 0, 'i'}, {"seqs", 1, 0, 's'}, {"exclude", 0, 0, 'x'}, {"no-probs", 0, 0, 'n'}, {"suff-stats", 0, 0, 'S'}, {"encode", 1, 0, 'e'}, {"keep-gaps", 0, 0, 'k'}, {"gibbs", 1, 0, 'G'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; /* arguments and defaults for options */ FILE *refseq_f = NULL; msa_format_type msa_format = UNKNOWN_FORMAT; int suff_stats = FALSE, exclude = FALSE, keep_gaps = FALSE, do_probs = TRUE; List *seqlist = NULL; PbsCode *code = NULL; int gibbs_nsamples = -1; while ((c = (char)getopt_long(argc, argv, "r:i:s:e:knxSh", long_opts, &opt_idx)) != -1) { switch (c) { case 'r': refseq_f = phast_fopen(optarg, "r"); break; case 'i': msa_format = msa_str_to_format(optarg); if (msa_format == UNKNOWN_FORMAT) die("ERROR: unrecognized alignment format.\n"); break; case 'S': suff_stats = TRUE; break; case 'e': code = pbs_new_from_file(phast_fopen(optarg, "r")); break; case 's': seqlist = get_arg_list(optarg); break; case 'x': exclude = TRUE; break; case 'n': do_probs = FALSE; break; case 'k': keep_gaps = TRUE; break; case 'G': gibbs_nsamples = get_arg_int_bounds(optarg, 1, INFTY); break; case 'h': printf("%s", HELP); exit(0); case '?': die("Bad argument. Try 'prequel -h'.\n"); } } if (optind != argc - 3) die("Three arguments required. Try 'prequel -h'.\n"); set_seed(-1); if (!do_probs && (suff_stats || code != NULL)) die("ERROR: --no-probs can't be used with --suff-stats or --encode.\n"); msa_f = phast_fopen(argv[optind], "r"); if (msa_format == UNKNOWN_FORMAT) msa_format = msa_format_for_content(msa_f, 1); fprintf(stderr, "Reading alignment from %s...\n", argv[optind]); if (msa_format == MAF) { msa = maf_read(msa_f, refseq_f, 1, NULL, NULL, NULL, -1, !suff_stats, NULL, NO_STRIP, FALSE); /* (no need to store order if suff_stats mode) */ } else msa = msa_new_from_file_define_format(msa_f, msa_format, NULL); if (msa->ss == NULL) { fprintf(stderr, "Extracting sufficient statistics...\n"); ss_from_msas(msa, 1, TRUE, NULL, NULL, NULL, -1, 0); } else if (msa->ss->tuple_idx == NULL && !suff_stats) die("ERROR: ordered representation of alignment required unless --suff-stats.\n"); mod_f = phast_fopen(argv[optind+1], "r"); out_root = argv[optind+2]; mod = tm_new_from_file(mod_f, 1); /* MH prune just like in phastcons */ int old_nnodes = mod->tree->nnodes; List *pruned_names = lst_new_ptr(msa->nseqs); tm_prune(mod, msa, pruned_names); if (lst_size(pruned_names) == (old_nnodes + 1) / 2) die("ERROR: no match for leaves of tree in alignment (leaf names must match alignment names).\n"); if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves of tree with no match in alignment ("); int j; for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); tr_name_ancestors(mod->tree); if (mod->order != 0) die("ERROR: Only single nucleotide models are supported.\n"); if (mod->nratecats > 1) die("ERROR: Rate variation not supported.\n"); mod->tree_posteriors = tl_new_tree_posteriors(mod, msa, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE); fprintf(stderr, "Computing posterior probabilities...\n"); if (gibbs_nsamples > 0) die("ERROR: --gibbs not implemented yet."); /* gb_sample_ancestral_seqs(mod, msa, mod->tree_posteriors, gibbs_nsamples); */ else tl_compute_log_likelihood(mod, msa, NULL, NULL, -1, mod->tree_posteriors); fprintf(stderr, "Reconstructing indels by parsimony...\n"); do_indels(msa, mod); for (node = 0; node < mod->tree->nnodes; node++) { int i, j; TreeNode *n = lst_get_ptr(mod->tree->nodes, node); if (n->lchild == NULL || n->rchild == NULL) continue; if (seqlist != NULL) { int in_list = str_in_list_charstr(n->name, seqlist); if ((in_list && exclude) || (!in_list && !exclude)) continue; } fprintf(stderr, "Writing output for ancestral node '%s'...\n", n->name); if (suff_stats) { if (out_f == NULL) { sprintf(out_fname, "%s.stats", out_root); out_f = phast_fopen(out_fname, "w+"); fprintf(out_f, "#count\t"); for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "p(%c)%c", mod->rate_matrix->states[j], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } for (i = 0; i < msa->ss->ntuples; i++) { if (mod->tree_posteriors->base_probs[0][0][node][i] == -1) continue; /* no base this node */ fprintf(out_f, "%.0f\t", msa->ss->counts[i]); for (j = 0; j < mod->rate_matrix->size; j++) { fprintf(out_f, "%f%c", mod->tree_posteriors->base_probs[0][j][node][i], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } } } else if (code == NULL && do_probs) { /* ordinary sequence-by-sequence output */ sprintf(out_fname, "%s.%s.probs", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); fprintf(out_f, "#"); for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "p(%c)%c", mod->rate_matrix->states[j], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); for (i = 0; i < msa->length; i++) { if (mod->tree_posteriors->base_probs[0][0][node][msa->ss->tuple_idx[i]] == -1) { /* no base */ if (keep_gaps) fprintf(out_f, "-\n"); /* otherwise do nothing */ } else for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "%f%c", mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } phast_fclose(out_f); } else if (code == NULL && !do_probs) { /* write point estimates to FASTA file */ char *outseq = smalloc((msa->length + 1) * sizeof(char)); int len = 0; for (i = 0; i < msa->length; i++) { if (mod->tree_posteriors->base_probs[0][0][node][msa->ss->tuple_idx[i]] == -1) { /* no base */ if (keep_gaps) outseq[len++] = GAP_CHAR; /* otherwise do nothing */ } else { double maxprob = 0; int maxidx = -1; for (j = 0; j < mod->rate_matrix->size; j++) { if (mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]] > maxprob) { maxprob = mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]]; maxidx = j; } } outseq[len++] = mod->rate_matrix->states[maxidx]; } } outseq[len] = '\0'; /* print in FASTA format */ sprintf(out_fname, "%s.%s.fa", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); print_seq_fasta(out_f, outseq, n->name, len); phast_fclose(out_f); sfree(outseq); } else { /* encoded sequence-by-sequence output */ double error, tot_error = 0; int ngaps = 0; Vector *v; unsigned *encoded; /* first encode tuple by tuple */ v = vec_new(mod->rate_matrix->size); encoded = smalloc(msa->ss->ntuples * sizeof(unsigned)); for (i = 0; i < msa->ss->ntuples; i++) { if (mod->tree_posteriors->base_probs[0][0][node][i] == -1) { encoded[i] = code->gap_code; ngaps += msa->ss->counts[i]; } else { for (j = 0; j < mod->rate_matrix->size; j++) vec_set(v, j, mod->tree_posteriors->base_probs[0][j][node][i]); encoded[i] = pbs_get_index(code, v, &error); tot_error += error * msa->ss->counts[i]; } } vec_free(v); /* now write site by site */ sprintf(out_fname, "%s.%s.bin", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); for (i = 0; i < msa->length; i++) { if (keep_gaps || encoded[msa->ss->tuple_idx[i]] != code->gap_code) pbs_write_binary(code, encoded[msa->ss->tuple_idx[i]], out_f); } fprintf(stderr, "Average approximation error ('%s'): %f bits\n", n->name, tot_error/(msa->length - ngaps)); sfree(encoded); } } fprintf(stderr, "Done.\n"); return 0; }
int main(int argc, char *argv[]) { char c; List *l; int i, j, strand, bed_output = 0, backgd_nmods = -1, feat_nmods = -1, winsize = -1, verbose = 0, max_nmods, memblocksize, old_nleaves, refidx = 1, base_by_base = FALSE, windowWig = FALSE; TreeModel **backgd_mods = NULL, **feat_mods = NULL; HMM *backgd_hmm = NULL, *feat_hmm = NULL; msa_format_type inform = UNKNOWN_FORMAT; GFF_Set *features = NULL; MSA *msa, *msa_compl=NULL; double **backgd_emissions, **feat_emissions, **mem, **dummy_emissions, *winscore_pos=NULL, *winscore_neg=NULL; int *no_alignment=NULL; List *pruned_names; char *msa_fname; FILE *infile; int opt_idx; struct option long_opts[] = { {"background-mods", 1, 0, 'b'}, {"background-hmm", 1, 0, 'B'}, {"feature-mods", 1, 0, 'f'}, {"feature-hmm", 1, 0, 'F'}, {"features", 1, 0, 'g'}, {"window", 1, 0, 'w'}, {"window-wig", 1, 0, 'W'}, {"base-by-base", 0, 0, 'y'}, {"msa-format", 1, 0, 'i'}, {"refidx", 1, 0, 'r'}, {"output-bed", 0, 0, 'd'}, {"verbose", 0, 0, 'v'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; while ((c = getopt_long(argc, argv, "B:b:F:f:r:g:w:W:i:ydvh", long_opts, &opt_idx)) != -1) { switch (c) { case 'B': backgd_hmm = hmm_new_from_file(phast_fopen(optarg, "r")); break; case 'b': l = get_arg_list(optarg); backgd_nmods = lst_size(l); backgd_mods = smalloc(backgd_nmods * sizeof(void*)); for (i = 0; i < backgd_nmods; i++) backgd_mods[i] = tm_new_from_file(phast_fopen(((String*)lst_get_ptr(l, i))->chars, "r"), 1); lst_free_strings(l); lst_free(l); break; case 'F': feat_hmm = hmm_new_from_file(phast_fopen(optarg, "r")); break; case 'f': l = get_arg_list(optarg); feat_nmods = lst_size(l); feat_mods = smalloc(feat_nmods * sizeof(void*)); for (i = 0; i < feat_nmods; i++) feat_mods[i] = tm_new_from_file(phast_fopen(((String*)lst_get_ptr(l, i))->chars, "r"), 1); lst_free_strings(l); lst_free(l); break; case 'g': features = gff_read_set(phast_fopen(optarg, "r")); break; case 'w': winsize = get_arg_int(optarg); if (winsize <= 0) die("ERROR: window size must be positive.\n"); break; case 'W': winsize = get_arg_int(optarg); if (winsize <= 0) die("ERROR: window size must be positive.\n"); windowWig = TRUE; break; case 'y': base_by_base = TRUE; break; case 'i': inform = msa_str_to_format(optarg); if (inform == UNKNOWN_FORMAT) die("Bad argument to -i.\n"); break; case 'r': refidx = get_arg_int_bounds(optarg, 0, INFTY); break; case 'd': bed_output = 1; break; case 'h': printf("%s", HELP); exit(0); case 'v': verbose = 1; break; case '?': die("Bad argument. Try '%s -h'.\n", argv[0]); } } set_seed(-1); if (backgd_mods == NULL || feat_mods == NULL) die("ERROR: -b and -f required. Try '%s -h'.\n", argv[0]); if (backgd_nmods == 1 && backgd_hmm == NULL) backgd_hmm = hmm_create_trivial(); else if (backgd_hmm == NULL) die("ERROR: -B required. Try '%s -h'.\n", argv[0]); if (feat_nmods == 1 && feat_hmm == NULL) feat_hmm = hmm_create_trivial(); else if (feat_hmm == NULL) die("ERROR: -F required. Try '%s -h'.\n", argv[0]); if ((winsize == -1 && features == NULL && !base_by_base) || (winsize != -1 && features != NULL) || (winsize != -1 && base_by_base) || (features != NULL && base_by_base)) die("ERROR: must specify exactly one of -g, -w, and -y. Try '%s -h'.\n", argv[0]); if (backgd_hmm->nstates != backgd_nmods) die("ERROR: number of states must equal number of tree models for background.\n"); if (feat_hmm->nstates != feat_nmods) die("ERROR: number of states must equal number of tree models for features.\n"); if (features != NULL && lst_size(features->features) == 0) die("ERROR: empty features file.\n"); if (base_by_base && (backgd_nmods > 1 || feat_nmods > 1)) die("ERROR: only single phylogenetic models (not HMMs) are supported with --base-by-base.\n"); if (optind != argc - 1) die("ERROR: too few arguments. Try '%s -h'.\n", argv[0]); if (verbose) fprintf(stderr, "Reading alignment ...\n"); msa_fname = argv[optind]; infile = phast_fopen(msa_fname, "r"); if (inform == UNKNOWN_FORMAT) inform = msa_format_for_content(infile, 1); if (inform == MAF) msa = maf_read(infile, NULL, 1, NULL, NULL, NULL, -1, TRUE, NULL, NO_STRIP, FALSE); else msa = msa_new_from_file_define_format(infile, inform, NULL); if (msa_alph_has_lowercase(msa)) msa_toupper(msa); msa_remove_N_from_alph(msa); /* need ordered representation of alignment */ if (msa->seqs == NULL && (msa->ss == NULL || msa->ss->tuple_idx == NULL) ) die("ERROR: ordered sufficient statistics are required.\n"); pruned_names = lst_new_ptr(msa->nseqs); for (i = 0; i < backgd_nmods; i++) { old_nleaves = (backgd_mods[i]->tree->nnodes + 1) / 2; tm_prune(backgd_mods[i], msa, pruned_names); if (lst_size(pruned_names) >= old_nleaves) die("ERROR: no match for leaves of tree in alignment (background model #%d)\n", i+1); else if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves in background model (#%d) with no match in alignment (", i+1); for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); } for (i = 0; i < feat_nmods; i++) { old_nleaves = (feat_mods[i]->tree->nnodes + 1) / 2; tm_prune(feat_mods[i], msa, pruned_names); if (lst_size(pruned_names) >= old_nleaves) die("ERROR: no match for leaves of tree in alignment (features model #%d)\n", i+1); else if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves in features model (#%d) with no match in alignment (", i+1); for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); } lst_free(pruned_names); /* first have to subtract offset from features, if necessary */ if (msa->idx_offset != 0 && features != NULL) { for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); f->start -= msa->idx_offset; f->end -= msa->idx_offset; } } /* convert to coord frame of alignment */ if (features != NULL && refidx != 0) { if (verbose) fprintf(stderr, "Mapping coordinates ...\n"); msa_map_gff_coords(msa, features, refidx, 0, 0); if (lst_size(features->features) == 0) die("ERROR: no features within coordinate range of alignment.\n"); } /* Make a reverse complemented copy of the alignment. The two strands will be processed separately, to avoid problems with overlapping features, etc. */ if (!base_by_base) { /* skip in base by base case */ if (verbose) fprintf(stderr, "Creating reverse complemented alignment ...\n"); msa_compl = msa_create_copy(msa, 0); /* temporary workaround: make sure reverse complement not based on sufficient stats */ if (msa_compl->seqs == NULL) ss_to_msa(msa_compl); if (msa_compl->ss != NULL) { ss_free(msa_compl->ss); msa_compl->ss = NULL; } msa_reverse_compl(msa_compl); } /* allocate memory for computing scores */ backgd_emissions = smalloc(backgd_nmods * sizeof(void*)); for (i = 0; i < backgd_nmods; i++) backgd_emissions[i] = smalloc(msa->length * sizeof(double)); feat_emissions = smalloc(feat_nmods * sizeof(void*)); for (i = 0; i < feat_nmods; i++) feat_emissions[i] = smalloc(msa->length * sizeof(double)); max_nmods = max(backgd_nmods, feat_nmods); dummy_emissions = smalloc(max_nmods * sizeof(void*)); mem = smalloc(max_nmods * sizeof(void*)); /* memory for forward algorithm -- each block must be as large as the largest feature */ if (features != NULL) { for (i = 0, memblocksize = -1; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); if (f->end - f->start + 1 > memblocksize) memblocksize = f->end - f->start + 1; } } else memblocksize = winsize; /* -1 if base-by-base mode */ if (memblocksize > 0) for (i = 0; i < max_nmods; i++) mem[i] = smalloc(memblocksize * sizeof(double)); if (winsize != -1) { winscore_pos = smalloc(msa->length * sizeof(double)); winscore_neg = smalloc(msa->length * sizeof(double)); no_alignment = smalloc(msa->length * sizeof(int)); for (i = 0; i < msa->length; i++) { winscore_pos[i] = winscore_neg[i] = NEGINFTY; if (refidx == 0) no_alignment[i] = FALSE; else no_alignment[i] = msa_missing_col(msa, refidx, i); } } /* the rest will be repeated for each strand */ for (strand = 1; strand <= 2; strand++) { MSA *thismsa = strand == 1 ? msa : msa_compl; double *winscore = strand == 1 ? winscore_pos : winscore_neg; if (base_by_base && strand == 2) break; /* don't do second pass in base_by_base case */ if (verbose) fprintf(stderr, "Processing %c strand ...\n", strand == 1 ? '+' : '-'); /* set up dummy categories array, so that emissions are only computed where needed */ thismsa->categories = smalloc(thismsa->length * sizeof(int)); thismsa->ncats = 1; if (winsize != -1) { if (strand == 1) for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = no_alignment[i] ? 0 : 1; else for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = no_alignment[thismsa->length - i - 1] ? 0 : 1; } else if (features != NULL) { for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = 0; for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); if (f->start <= 0 || f->end <= 0) { fprintf(stderr, "WARNING: feature out of range ('"); gff_print_feat(stderr, f); fprintf(stderr, "')\n"); continue; } if (strand == 1 && f->strand != '-') for (j = f->start - 1; j < f->end; j++) thismsa->categories[j] = 1; else if (strand == 2 && f->strand == '-') for (j = thismsa->length - f->end; j < thismsa->length - f->start + 1; j++) thismsa->categories[j] = 1; } } else { /* base-by-base scores */ for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = 1; } if (thismsa->ss != NULL) ss_update_categories(thismsa); /* compute emissions */ for (i = 0; i < backgd_nmods; i++) { if (verbose) fprintf(stderr, "Computing emissions for background model #%d ...\n", i+1); tl_compute_log_likelihood(backgd_mods[i], thismsa, backgd_emissions[i], NULL, 1, NULL); } for (i = 0; i < feat_nmods; i++) { if (verbose) fprintf(stderr, "Computing emissions for features model #%d ...\n", i+1); tl_compute_log_likelihood(feat_mods[i], thismsa, feat_emissions[i], NULL, 1, NULL); } /* now compute scores */ if (winsize != -1) { /* windows case */ int winstart; if (verbose) fprintf(stderr, "Computing scores ...\n"); for (winstart = 0; winstart <= thismsa->length - winsize; winstart++) { int centeridx = winstart + winsize/2; if (strand == 2) centeridx = thismsa->length - centeridx - 1; if (no_alignment[centeridx]) continue; for (j = 0; j < feat_nmods; j++) dummy_emissions[j] = &(feat_emissions[j][winstart]); winscore[centeridx] = hmm_forward(feat_hmm, dummy_emissions, winsize, mem); if (winscore[centeridx] <= NEGINFTY) { winscore[centeridx] = NEGINFTY; continue; } for (j = 0; j < backgd_nmods; j++) dummy_emissions[j] = &(backgd_emissions[j][winstart]); winscore[centeridx] -= hmm_forward(backgd_hmm, dummy_emissions, winsize, mem); if (winscore[centeridx] < NEGINFTY) winscore[centeridx] = NEGINFTY; } } else if (features != NULL) { /* features case */ if (verbose) fprintf(stderr, "Computing scores ...\n"); for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); int s, e; if ((strand == 1 && f->strand == '-') || (strand == 2 && f->strand != '-') || f->start <= 0 || f->end <= 0 || f->end - f->start < 0) continue; /* effective coords */ if (f->strand == '-') { s = thismsa->length - f->end + 1; e = thismsa->length - f->start + 1; } else { s = f->start; e = f->end; } f->score_is_null = 0; for (j = 0; j < feat_nmods; j++) dummy_emissions[j] = &(feat_emissions[j][s-1]); f->score = hmm_forward(feat_hmm, dummy_emissions, e - s + 1, mem); if (f->score <= NEGINFTY) { f->score = NEGINFTY; continue; } for (j = 0; j < backgd_nmods; j++) dummy_emissions[j] = &(backgd_emissions[j][s-1]); f->score -= hmm_forward(backgd_hmm, dummy_emissions, e - s + 1, mem); if (f->score < NEGINFTY) f->score = NEGINFTY; } } } if (verbose) fprintf(stderr, "Generating output ...\n"); if (winsize != -1 && windowWig == FALSE) { /* standard windows output */ for (i = 0, j = 0; i < msa->length; i++) { if (no_alignment[i] == FALSE) printf("%d\t%.3f\t%.3f\n", j + msa->idx_offset + 1, winscore_pos[i], winscore_neg[i]); if (ss_get_char_pos(msa, i, 0, 0) != GAP_CHAR) j++; } } else if (windowWig == TRUE) { /* windows with wig output */ int last = NEGINFTY; for (i = 0, j = 0; i < msa->length; i++) { if (refidx == 0 || msa_get_char(msa, refidx-1, i) != GAP_CHAR) { if (no_alignment[i] == FALSE && winscore_pos[i] > NEGINFTY) { if (j > last + 1) printf("fixedStep chrom=%s start=%d step=1\n", refidx > 0 ? msa->names[refidx-1] : "alignment", j + msa->idx_offset + 1); printf("%.3f\n", winscore_pos[i]); last = j; } j++; } } } else if (features != NULL) { /* features output */ /* return to coord frame of reference seq (also, replace offset) */ if (refidx != 0) msa_map_gff_coords(msa, features, 0, refidx, msa->idx_offset); else if (msa->idx_offset != 0) { for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); f->start += msa->idx_offset; f->end += msa->idx_offset; } } if (bed_output) gff_print_bed(stdout, features, FALSE); else gff_print_set(stdout, features); } else { /* base-by-base scores */ /* in this case, we can just output the difference between the emissions */ printf("fixedStep chrom=%s start=%d step=1\n", refidx > 0 ? msa->names[refidx-1] : "alignment", msa->idx_offset + 1); for (i = 0, j = 0; i < msa->length; i++) { if (refidx == 0 || msa_get_char(msa, refidx-1, i) != GAP_CHAR) { printf("%.3f\n", feat_emissions[0][i] - backgd_emissions[0][i]); j++; } } } if (verbose) fprintf(stderr, "\nDone.\n"); return 0; }