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

mkdir tih_rna_sample_00096_23H5VFLT4_s11

all_qc \
-bam "tih_rna_sample_00096_23H5VFLT4_s11.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 tih_rna_sample_00096_23H5VFLT4_s11 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders tih_rna_sample_00096_23H5VFLT4_s11/* -output tih_rna_sample_00096_23H5VFLT4_s11/tih_rna_sample_00096_23H5VFLT4_s11_full_basic_stats.tsv

head -n1 tih_rna_sample_00096_23H5VFLT4_s11/tih_rna_sample_00096_23H5VFLT4_s11_full_basic_stats.tsv > tih_rna_sample_00096_23H5VFLT4_s11/tih_rna_sample_00096_23H5VFLT4_s11_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" tih_rna_sample_00096_23H5VFLT4_s11/tih_rna_sample_00096_23H5VFLT4_s11_full_basic_stats.tsv >> tih_rna_sample_00096_23H5VFLT4_s11/tih_rna_sample_00096_23H5VFLT4_s11_basic_stats.tsv