get_rid_of_VEP's_problem.sh

### Clear the Parent info ###
sed -i 's/;Parent=.*//g' mushroom_remove_parent.gff3
### Clear the scaffold size info incase the error in the output html report file ###
sed -i 's/|size[0-9]*//g' ${ID}.vcf
sed -i 's/|size[0-9]*//g' mushroom_remove_parent.gff3
sed -i 's/|size[0-9]*//g' mushroom_clear_scaffold.fasta
### Add additional "0" to avoid the sort problem in html report file ###
sed -r 's/scaffold[0-9]{1}\b/scaffold0&/g' ${ID}.vcf | sed -r 's/0scaffold/0/g' > ${ID}_add_zero
sed -r 's/scaffold/scaffold\t/g' mushroom_remove_parent.gff3 | sed -r 's/\t[0-9]{1}\t/0&/g' > mushroom_add_zero.gff3
sed -r 's/scaffold[0-9]{1}\b/scaffold0&/g' mushroom_clear_scaffold.fasta | sed -r 's/0scaffold/0/g' > mushroom_add_zero.fasta

### Finally we can run VEP to output report ###
vep -i ${ID}_add_zero -gff ${genomeDir}/${gffName}.gff.gz -fasta ${genomeDir}/${genomeFile}.gz -o ${ID}_variant_effect.txt