R/RcppExports.R

In HIVDiversity/MotifBinner2: Processes NGS Primer ID Datasets

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

pairWiseMSA_cpp <- function(r_sread, r_ref_seq, r_seq_names) {
    .Call('_MotifBinner2_pairWiseMSA_cpp', PACKAGE = 'MotifBinner2', r_sread, r_ref_seq, r_seq_names)
}

trimFront_cpp <- function(r_sread, r_qual, r_primer, prefix_lens) {
    .Call('_MotifBinner2_trimFront_cpp', PACKAGE = 'MotifBinner2', r_sread, r_qual, r_primer, prefix_lens)
}

map_reads_no_ins_cpp <- function(r_profile, r_reads, r_quals) {
    .Call('_MotifBinner2_map_reads_no_ins_cpp', PACKAGE = 'MotifBinner2', r_profile, r_reads, r_quals)
}

transfer_gaps_cpp <- function(aligned_read, r_qual, gap_only_cols) {
    .Call('_MotifBinner2_transfer_gaps_cpp', PACKAGE = 'MotifBinner2', aligned_read, r_qual, gap_only_cols)
}

gapQualityTweaker_ol_cpp <- function(reads, q_mat) {
    .Call('_MotifBinner2_gapQualityTweaker_ol_cpp', PACKAGE = 'MotifBinner2', reads, q_mat)
}

gapQualityTweaker_non_ol_cpp <- function(reads, q_mat, which_pair, avg_quals) {
    .Call('_MotifBinner2_gapQualityTweaker_non_ol_cpp', PACKAGE = 'MotifBinner2', reads, q_mat, which_pair, avg_quals)
}

scoreAlignmentPositions_cpp <- function(reads, q_mat) {
    .Call('_MotifBinner2_scoreAlignmentPositions_cpp', PACKAGE = 'MotifBinner2', reads, q_mat)
}

buildConsensus_cpp <- function(score_mat, required_dominance, minimum_score) {
    .Call('_MotifBinner2_buildConsensus_cpp', PACKAGE = 'MotifBinner2', score_mat, required_dominance, minimum_score)
}

tallyPrimerSeqErrors_cpp <- function(r_sread, r_primer, r_qual) {
    .Call('_MotifBinner2_tallyPrimerSeqErrors_cpp', PACKAGE = 'MotifBinner2', r_sread, r_primer, r_qual)
}

regionSplit_cpp <- function(mapped_read, profile, region_map, mapped_qual) {
    .Call('_MotifBinner2_regionSplit_cpp', PACKAGE = 'MotifBinner2', mapped_read, profile, region_map, mapped_qual)
}

removeChars_cpp <- function(r_sread, r_qual, char_to_strip) {
    .Call('_MotifBinner2_removeChars_cpp', PACKAGE = 'MotifBinner2', r_sread, r_qual, char_to_strip)
}