When the input sequences are not sorted fully by length, bedtools maskfasta can generate a multi-line fasta file which btllib SeqReader has issues with reading
To solve it, added a seqtk seq step to ensure the bedtools output fastas are single-line prior to downstream steps
bedtools maskfastacan generate a multi-line fasta file which btllib SeqReader has issues with readingseqtk seqstep to ensure thebedtoolsoutput fastas are single-line prior to downstream steps