remote/bin/ont-basecalling-model-info @ 26c18ba81503

#!/usr/bin/env bash

set -euo pipefail

bam_file="$1"

module load Bioinformatics samtools >/dev/null 2>&1

#     view all the SAM headers
#     only look at @RG
#     pull out the basecall_model=… field
#     coalesce

samtools view -H "$bam_file" \
    | grep -P '^@RG' \
    | grep -P -o $'basecall_model=[^ \t]+' \
    | sort | uniq -c

samtools view -H "$bam_file" \
    | grep -P '^@RG' \
    | grep -P -o $'modbase_models=[^ \t]+' \
    | sort | uniq -c