Refactoring of code https://github.com/genepi/haplocheck such that it takes vcf file containing directory from command line outside the cloudgene framework
Compile
jar cvfe haplocheckCLI.jar haplocheck_contam *
Usage
java -jar haplocheckCLI.jar directory_with_vcf
TO DO
Switch back from VL to AF
Get rid of those annoying double quotes in output
Other cool stuff