#!/bin/bash -Ceuo pipefail
mkdir -p normalized/1029_0I baf
ln -s $(pwd)/1029_0I-T1-TDNA-1_A23KCGYLT4_1_normalized.parquet normalized/1029_0I/1029_0I-T1-TDNA-1_A23KCGYLT4_1.parquet
ln -s $(pwd)/1029_0I-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet normalized/1029_0I/1029_0I-N1-BDNA-1_B23KGCJLT4_1.parquet
zcat 1029_0I-T1-TDNA-1_A23KCGYLT4_1_alleles.tsv.gz > baf/1029_0I-T1-TDNA-1_A23KCGYLT4_1.tsv
zcat 1029_0I-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz > baf/1029_0I-N1-BDNA-1_B23KGCJLT4_1.tsv

python /usr/local/bin/export_viewer.py \
    --normalized-dir normalized \
    --pairs test_pairs.tsv \
    --segments 1029_0I_segments.tsv \
    --output-dir viewer \
    --baf baf \
    --specimens-file <(echo "1029_0I") \
    --workers 4