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

mkdir BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2

all_qc \
-bam "BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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 BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/* -output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_full_basic_stats.tsv

head -n1 BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_full_basic_stats.tsv > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_full_basic_stats.tsv >> BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_basic_stats.tsv