#!/bin/env bash

for sample in $(cat hifiasm_ont_v0.19.6_assemblies_batch2.fofn | awk -F "/" '{print $11}' | sort | uniq); do
	echo ${sample}
	cp /net/eichler/vol28/projects/hgsvc/nobackups/sharing/assemblies/20240318_hifiasm_ont_batch2/${sample}/${sample}-hifiasm-hap*.fasta.gz ./
	gunzip ${sample}-hifiasm-hap*.fasta.gz
	cat ${sample}-hifiasm-hap*.fasta > ${sample}-hifiasm_v0.19.6.fa
	rm ${sample}-hifiasm-hap*.fasta
	#gzip ${sample}-hifiasm_v0.19.6.fa
done
