#!/bin/bash -Ceuo pipefail
set -euo pipefail
/usr/local/bin/make_freq_file \
    --bam-file 'three.deduped.bam' \
    --output-file three.deduped.freqs.txt \
    --duplex three.deduped.freqs.duplex.txt \
    --reference-file 'hg38.fa' \
    --bed-file 'small_padded.bed' \
    --unpad-bed-file 'small.bed' \
    --threads 4 \
    --duplex-tag "XX" \
    --min-bq 30 \
    --min-mapq 30 \
    --tabix