HardMaskFasta

Overview

Group: FASTA

Converts soft-masked sequence to hard-masked in a FASTA file. All lower case bases are converted to Ns, all other bases are left unchanged. Line lengths are also standardized to allow easy indexing with samtools faidx”

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToFasta	Input FASTA file.	Required	1
output	o	PathToFasta	Output FASTA file.	Required	1
line-length	l	Int	Line length or sequence lines.	Optional	1	100