Script to generate template VCF file for assembly

[timothymillar]

Simple script to generate a template VCF for MCHap assemble.

There are several motivations for this:

• Simplicity, we only need position and alleles of putative segregating sites
• Speed, less compute and using same input files
• Ability to mask reference allele to lower parameter space #165

[timothymillar]

Idea for arguments:

• --maf: min population allele frequency (default = 0.0)
• --mad: min population allele depth (default = 0)
• --ind-maf: min individual allele frequency (default = 0.1)
• --ind-mad: min individual allele depth (default = 3)
• --ind-min: min number of individuals passing --ind-maf and --ind-mad (default = 1)

All filters are combined (intersection). This gives good flexibility and makes few assumptions about population size/structure for defaults.

[timothymillar]

Fixed in #169