process_allele
is used to returned the processed allelic profiles, by
removing the allele profile with duplicate name and length different
from most. 1st allele profile with the duplicated name is returned,
the longer length is taken as normal should there be 2 modes.
process_allele(
seqc,
bp = BiocParallel::SerialParam(),
check_length = TRUE,
check_bases = TRUE,
dash_ignore = TRUE,
accepted_char = c("A", "C", "T", "G"),
ignore_case = TRUE,
remove_invariant = FALSE,
biallelic_only = FALSE
)
a list containing list of nucleotides. To keep it simple, use provided read_fasta to import the fasta file.
is the biocparallel backend, default to serialParam, most likely sufficient in most scenario
Check the length of each sample in the matrix, default to TRUE
Check the bases of each sample in the matrix, default to TRUE
whether to treat '-' as another type
character to accept, default to c("A", "C", "T", "G")
whether to be case insensitive, default to TRUE
whether to remove invariant positions, default to FALSE
whether to remove positions with more than 2 alleles, default to FALSE
Will return the processed allelic profiles.