R/RcppExports.R

In BBCG/epialleleR: Fast, Epiallele-Aware Methylation Caller and Reporter

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

rcpp_call_methylation_genome <- function(in_fn, out_fn, genome, tag, nthreads) {
    .Call(`_epialleleR_rcpp_call_methylation_genome`, in_fn, out_fn, genome, tag, nthreads)
}

rcpp_check_bam <- function(fn) {
    .Call(`_epialleleR_rcpp_check_bam`, fn)
}

rcpp_cx_report <- function(df, pass, ctx) {
    .Call(`_epialleleR_rcpp_cx_report`, df, pass, ctx)
}

rcpp_extract_patterns <- function(df, target_rname, target_start, target_end, min_overlap, ctx, min_ctx_freq, clip, reverse_offset, hlght) {
    .Call(`_epialleleR_rcpp_extract_patterns`, df, target_rname, target_start, target_end, min_overlap, ctx, min_ctx_freq, clip, reverse_offset, hlght)
}

rcpp_fep <- function(df, colnames) {
    .Call(`_epialleleR_rcpp_fep`, df, colnames)
}

rcpp_get_base_freqs <- function(df, pass, vcf) {
    .Call(`_epialleleR_rcpp_get_base_freqs`, df, pass, vcf)
}

rcpp_get_xm_beta <- function(df, ctx_meth, ctx_unmeth) {
    .Call(`_epialleleR_rcpp_get_xm_beta`, df, ctx_meth, ctx_unmeth)
}

rcpp_match_amplicon <- function(df, bed, tolerance) {
    .Call(`_epialleleR_rcpp_match_amplicon`, df, bed, tolerance)
}

rcpp_match_capture <- function(df, bed, min_overlap) {
    .Call(`_epialleleR_rcpp_match_capture`, df, bed, min_overlap)
}

rcpp_mhl_report <- function(df, ctx, hmax, hmin, max_ooctx_meth_frac) {
    .Call(`_epialleleR_rcpp_mhl_report`, df, ctx, hmax, hmin, max_ooctx_meth_frac)
}

rcpp_read_bam_paired <- function(fn, min_mapq, min_baseq, skip_duplicates, trim5, trim3, nthreads) {
    .Call(`_epialleleR_rcpp_read_bam_paired`, fn, min_mapq, min_baseq, skip_duplicates, trim5, trim3, nthreads)
}

rcpp_read_bam_single <- function(fn, min_mapq, min_baseq, skip_duplicates, trim5, trim3, nthreads) {
    .Call(`_epialleleR_rcpp_read_bam_single`, fn, min_mapq, min_baseq, skip_duplicates, trim5, trim3, nthreads)
}

rcpp_read_bam_mm_single <- function(fn, min_mapq, min_baseq, min_prob, highest_prob, skip_duplicates, trim5, trim3, nthreads) {
    .Call(`_epialleleR_rcpp_read_bam_mm_single`, fn, min_mapq, min_baseq, min_prob, highest_prob, skip_duplicates, trim5, trim3, nthreads)
}

rcpp_read_genome <- function(fn, nthreads) {
    .Call(`_epialleleR_rcpp_read_genome`, fn, nthreads)
}

rcpp_simulate_bam <- function(header, fields, i_tags, f_tags, s_tags, a_tags, a_types, out_fn) {
    .Call(`_epialleleR_rcpp_simulate_bam`, header, fields, i_tags, f_tags, s_tags, a_tags, a_types, out_fn)
}

rcpp_threshold_reads <- function(df, ctx_meth, ctx_unmeth, ooctx_meth, ooctx_unmeth, min_n_ctx, min_ctx_meth_frac, max_ooctx_meth_frac) {
    .Call(`_epialleleR_rcpp_threshold_reads`, df, ctx_meth, ctx_unmeth, ooctx_meth, ooctx_unmeth, min_n_ctx, min_ctx_meth_frac, max_ooctx_meth_frac)
}