paraMrBam

#!/usr/bin/env bash

if [[ $# -eq 0 ]] ; then
    echo "usage: paraMrBam 16 input.vcf [options for MrBam, except vcf, -o and --skip] > output.vcf"
    echo "if second argument ends in .txt, it will skip the first line automatically"
    exit 1
fi

export PYTHONPATH=/haplox/users/wangzy/Software

TMP=$(mktemp -d)
cd $CWD
vcf=$2

for i in "$@"; do
    if [ $i = "--snp" ];then
    #echo "/usr/bin/python3 -m MrBam.main ${@:2} --continous -o $TMP/continous_MrBam.txt > $TMP/breaked.snp.txt"
	/usr/bin/python3 -m MrBam.main ${@:2} --continous -o $TMP/continous_MrBam.txt > $TMP/breaked.snp.txt
	#/data/haplox/users/wangzy/00.Tools/02.HGVS.parse/HGVS.parser.py $TMP/continous_MrBam.txt > $TMP/continous_HGVS.MrBam.txt 
	# rm $TMP/continous_MrBam.txt
    vcf=$TMP/breaked.snp.txt
    fi
done

echo $(head -n 1 $vcf)
let LINE=($(wc -l < $vcf)+ $1-1)/$1
tail $vcf -n +2 | split -l $LINE - $TMP/

for i in $TMP/*; do
    if [ $i != $TMP/breaked.snp.txt ];then 
        if [ $i != $TMP/continous_MrBam.txt ];then
            /usr/bin/python3 -m MrBam.main  ${@:3} $i & 
        fi
    fi
done
wait

cat $TMP/*_MrBam*
rm -rf $TMP