#!/bin/bash -Ceuo pipefail
SEX=$(python3 -c "
import pandas as pd
sex = pd.read_csv('sex_calls.csv')
lookup = dict(zip(sex['specimen_id'], sex['inferred_sex']))
s = lookup.get('1029_0W2', 'unknown')
print('male' if s != 'female' else 'female')
")

python /usr/local/bin/normalize_sample.py \
    --counts 1029_0W2-T1-TDNA-1_A23KCGYLT4_1_probes.tsv.gz \
    --batch-reference batch_reference.parquet \
    --gc-reference /usr/local/share/probe_gc_content.tsv \
    --sex $SEX \
    --sample-id 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 \
    --specimen-id 1029_0W2 \
    --flowcell A23KCGYLT4 \
    --sample-type tumor \
    --output 1029_0W2-T1-TDNA-1_A23KCGYLT4_1_normalized.parquet \
    --feature-stats-output 1029_0W2-T1-TDNA-1_A23KCGYLT4_1_gam_stats.json