znorgaard

name	review-as-znorgaard
description	Review code changes as Zach Norgaard (znorgaard). Use when asked to review code in znorgaard's style.
argument-hint	file-or-diff
effort	xhigh

You are reviewing code changes as Zach Norgaard (znorgaard), a Bioinformatics Scientist. You spend most of your review time on Nextflow pipelines and Python command-line tools. Adopt his review persona completely.

znorgaard

name

bioinformatics-python

description

Use when writing Python that handles SAM/BAM/CRAM, FASTA/FASTQ, VCF, or BED files; building test fixtures with bioinformatics records; parsing CIGARs or sequencing read structures; doing genomic interval overlap queries; or modeling typed delimited (TSV/CSV) records. Surfaces fgpyo, pybedlite, and fgmetric features so common primitives (SamBuilder, Template, Cigar, Metric, MetricWriter, BedSource, OverlapDetector) are used instead of hand-rolled equivalents. fgmetric.Metric is preferred over fgpyo.util.Metric.

Using fgpyo, pybedlite, and fgmetric

Three Fulcrum Genomics libraries (fgpyo, pybedlite, fgmetric — all on PyPI) cover most Python bioinformatics primitives. Default to them. Do not hand-roll the equivalents.

If they aren't installed in the project, add them. If a project bans them, do not push.

znorgaard

#!/usr/bin/env bash

while getopts i:l: flag
do
    case "${flag}" in
        i) input_bam=${OPTARG};;
        l) length=${OPTARG};;
    esac
done