haps_vcf {jackalope}

Organize information to create haplotypes using a VCF file

Description

This function organizes higher-level information for creating haplotypes from Variant Call Format (VCF) files.

Usage

haps_vcf(fn, print_names = FALSE)

Arguments

fn

A single string specifying the name of the VCF file

print_names

Logical for whether to print all unique chromosome names from the VCF file when VCF chromosome names don't match those from the reference genome. This printing doesn't happen until this object is passed to create_haplotypes. This can be useful for troubleshooting. Defaults to FALSE.

Value

A haps_vcf_info object containing information used in create_haplotypes to create variant haplotypes. This class is just a wrapper around a list containing the arguments to this function, which you can view (but not change) using the object's fn() and print_names() methods.