write_region_file: Write temporary loci region file

Description Usage Arguments Value

Description

write_region_file creates the file needed by samtools faidx to get the k surrounding bases of the loci defined in mutation_ids.

Usage

1
write_region_file(ids, k, tmp_filename)

Arguments

ids

character vector containing the ids of the loci to get the surrounding bases of. Id format is CHR:POS and can be obtained by calling the function get_mut_id on the vcf file containing those loci.

k

integer with the number of bases to the right and to the left of the loci to get the genomic sequence from.

tmp_filename

character string naming the path to the file to write.

Value

None


mmaitenat/ideafix documentation built on Sept. 18, 2021, 7:55 a.m.