#!/bin/bash -euo pipefail
set -euxo pipefail

mkdir A549_FFPE_01_RNA_0001_B23LG7FLT4_3

all_qc \
-bam "A549_FFPE_01_RNA_0001_B23LG7FLT4_3.md.bam" \
-beds Twist_rna_exome_AND_fusion_hg38.bed \
-dbsnp_vcf "Homo_sapiens_assembly38.dbsnp138.vcf.gz" \
-contamination_bed "dbsnp_hg38_contam_sites.bed" \
-output_folder A549_FFPE_01_RNA_0001_B23LG7FLT4_3 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders A549_FFPE_01_RNA_0001_B23LG7FLT4_3/* -output A549_FFPE_01_RNA_0001_B23LG7FLT4_3/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv

head -n1 A549_FFPE_01_RNA_0001_B23LG7FLT4_3/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv > A549_FFPE_01_RNA_0001_B23LG7FLT4_3/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" A549_FFPE_01_RNA_0001_B23LG7FLT4_3/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv >> A549_FFPE_01_RNA_0001_B23LG7FLT4_3/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_basic_stats.tsv