Haplotype counting script

A simple script for counting of a number of haplotypes formed by pre-selected SNPs in long-read sequencing data. The number of haplotypes is counted per 1kb in individual long sequencing reads aligned to a reference, based on the position, reference and alternative alleles of reliable SNPs called on short-read sequencing data

Required input files: 

- processed long sequencing reads aligned to the reference and split per chromosome/contig into individual files - the names must correspond with the respective vcf files 

- vcf files with reliable biallelic SNPs split per chromosome/contig into individual files - the names must correspond with the respective bam files 

- file with names for each chromosome/contig -  has to be the same as names for bam and vcf files

Required software: 
- Java version 1.8 or higher

- downloaded and compiled sam2tsv.jar from jvarkit https://github.com/lindenb/jvarkit