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

mkdir BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1

all_qc \
-bam "BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.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 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/* -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv

head -n1 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv >> BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_basic_stats.tsv