hap-ibd to bed file (not plink bed, just normal genome track bed)

gistfile1.txt

#!/bin/bash

# create a bed file from hap-ibd output with columns "chr, start, end, sample_name1 hap1 sample_name2 hap2"
# add this config to jbrowse get(feature,'sample1')+':HP'+get(feature,'hap1')+'     '+get(feature,'sample2')+':HP'+get(feature,'hap2')

# Process file in a fully streaming fashion and pipe directly to bgzip
# Combine header and data in a single stream
(
  echo -e "#chr\tstart\tend\tsample1\thap1\tsample2\thap2"
  zcat "$1" | awk -F'\t' '{print $5"\t"$6"\t"$7"\t"$1"\t"$2"\t"$3"\t"$4}'
) | bgzip -@8 >out.bed.gz