#!/bin/bash -Ceuo pipefail
# Matplotlib cache dir must be writable; default location may not be
export MPLCONFIGDIR=/tmp/matplotlib

all_qc \
    -bam HCC1395_tumor.md.bam \
    -reference Homo_sapiens_assembly38.fasta \
    -beds xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed foresight_clarity_targets_hg38.bed \
    -dbsnp_bed dbsnp138_hg38_common.bed \
    -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz \
    -contamination_bed dbsnp_hg38_contam_sites.bed \
    -output_folder HCC1395_tumor \
    -threads 31 \


merge_qc -folders HCC1395_tumor/* -output HCC1395_tumor/HCC1395_tumor_full_basic_stats.tsv

head -n1 HCC1395_tumor/HCC1395_tumor_full_basic_stats.tsv > HCC1395_tumor/HCC1395_tumor_basic_stats.tsv
grep -e "$(basename xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed)" HCC1395_tumor/HCC1395_tumor_full_basic_stats.tsv >> HCC1395_tumor/HCC1395_tumor_basic_stats.tsv

cat <<-END_VERSIONS > versions.yml
"DAQ:BAM_POSTDEDUP_QC:SEQTOOL":
    seqtool: 2.0
END_VERSIONS