SEXP mdmr_fstats_to_pvals(SEXP SFmat) { try { arma::mat Fmat(1,1); const double* old_fptr = sbm_to_arma_xd(SFmat, Fmat); double nvoxs = static_cast<double>(Fmat.n_cols); double nperms = static_cast<double>(Fmat.n_rows); Rcpp::NumericVector pvals(nvoxs); // original F-stats arma::rowvec realFs = Fmat.row(0); double i; for (i = 0; i < nvoxs; ++i) { pvals[i] = arma::as_scalar(arma::sum(Fmat.col(i) >= realFs(i))/nperms); } free_arma(Fmat, old_fptr); return Rcpp::wrap( pvals );; } catch(std::exception &ex) { forward_exception_to_r(ex); } catch(...) { ::Rf_error("c++ exception (unknown reason)"); } return R_NilValue; }
static int trim_ns(bam1_t *b, void *data) { int ret = 0; opts_t *op((opts_t *)data); std::vector<uint8_t> aux(bam_get_aux(b), bam_get_aux(b) + bam_get_l_aux(b)); int tmp; uint8_t *const seq(bam_get_seq(b)); uint32_t *const cigar(bam_get_cigar(b)); //op->n_cigar = b->core.n_cigar; op->resize(b->l_data); // Make sure it's big enough to hold everything. memcpy(op->data, b->data, b->core.l_qname); // Get #Ns at the beginning for(tmp = 0; bam_seqi(seq, tmp) == dlib::htseq::HTS_N; ++tmp); const int n_start(tmp); if(tmp == b->core.l_qseq - 1) // all bases are N -- garbage read ret |= op->skip_all_ns; // Get #Ns at the end for(tmp = b->core.l_qseq - 1; bam_seqi(seq, tmp) == dlib::htseq::HTS_N; --tmp); const int n_end(b->core.l_qseq - 1 - tmp); // Get new length for read int final_len(b->core.l_qseq - n_end - n_start); if(final_len < 0) final_len = 0; if(final_len < op->min_trimmed_len) // Too short. ret |= 1; // Copy in qual and all of aux. if(n_end) { if((tmp = bam_cigar_oplen(cigar[b->core.n_cigar - 1]) - n_end) == 0) { LOG_DEBUG("Entire cigar operation is the softclip. Decrease the number of new cigar operations.\n"); --b->core.n_cigar; } else { LOG_DEBUG("Updating second cigar operation in-place.\n"); cigar[b->core.n_cigar - 1] = bam_cigar_gen(tmp, BAM_CSOFT_CLIP); } } // Get new n_cigar. if((tmp = bam_cigar_oplen(*cigar) - n_start) == 0) { memcpy(op->data + b->core.l_qname, cigar + 1, (--b->core.n_cigar) << 2); // << 2 for 4 bit per cigar op } else { if(n_start) *cigar = bam_cigar_gen(tmp, BAM_CSOFT_CLIP); memcpy(op->data + b->core.l_qname, cigar, b->core.n_cigar << 2); } uint8_t *opseq(op->data + b->core.l_qname + (b->core.n_cigar << 2)); // Pointer to the seq region of new data field. for(tmp = 0; tmp < final_len >> 1; ++tmp) opseq[tmp] = (bam_seqi(seq, ((tmp << 1) + n_start)) << 4) | (bam_seqi(seq, (tmp << 1) + n_start + 1)); if(final_len & 1) opseq[tmp] = (bam_seqi(seq, ((tmp << 1) + n_start)) << 4); tmp = bam_get_l_aux(b); memcpy(opseq + ((final_len + 1) >> 1), bam_get_qual(b) + n_start, final_len + tmp); // Switch data strings std::swap(op->data, b->data); b->core.l_qseq = final_len; memcpy(bam_get_aux(b), aux.data(), aux.size()); b->l_data = (bam_get_aux(b) - b->data) + aux.size(); if(n_end) bam_aux_append(b, "NE", 'i', sizeof(int), (uint8_t *)&n_end); if(n_start) bam_aux_append(b, "NS", 'i', sizeof(int), (uint8_t *)&n_start); const uint32_t *pvar((uint32_t *)dlib::array_tag(b, "PV")); tmp = b->core.flag & BAM_FREVERSE ? n_end: n_start; if(pvar) { std::vector<uint32_t>pvals(pvar + tmp, pvar + final_len + tmp); bam_aux_del(b, (uint8_t *)(pvar) - 6); dlib::bam_aux_array_append(b, "PV", 'I', sizeof(uint32_t), final_len, (uint8_t *)pvals.data()); } const uint32_t *fvar((uint32_t *)dlib::array_tag(b, "FA")); if(fvar) { std::vector<uint32_t>fvals(fvar + tmp, fvar + final_len + tmp); bam_aux_del(b, (uint8_t *)(fvar) - 6); dlib::bam_aux_array_append(b, "FA", 'I', sizeof(uint32_t), final_len, (uint8_t *)fvals.data()); } return ret; }