Impute from VCF

[ClayBirkett]

Description

The VCF file and reference assembly is used to create a fastq file for each sample in the VCF. These fastq files can then be used to run the normal pipeline

#235

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• CHANGE (fix or feature that would cause existing functionality to not work as expected)
• [x ] FEATURE (non-breaking change which adds functionality)
• BUGFIX (non-breaking change which fixes an issue)
• ENHANCEMENT (non-breaking change which improves existing functionality)
• NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• I have performed a self-review of my code
• [x ] I have commented my code, particularly in hard-to-understand areas
• [ x] I have updated relevant documentation

Changelog entry

Impute from VCF file

Added a new command "map-reads-vcf" to impute from VCF file