#!/usr/bin/env bash
# H1 genome-wide: run the per-chromosome H1 pipeline for all autosomes (chr1..22).
# Idempotent — skips chroms already trained. Disables per-chrom figures by default
# (set SKIP_FIGURES= to enable).
#
# Usage:
#   bash experiments/h1_representation/run_genome.sh
#   bash experiments/h1_representation/run_genome.sh chr2 chr5    # only these
#   SKIP_FIGURES= bash experiments/h1_representation/run_genome.sh  # render figures
set -euo pipefail

REPO="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"

# Skip per-chrom UMAP/compare figures during genome loop (slow; render manually
# for representative chroms after aggregation).
export SKIP_FIGURES="${SKIP_FIGURES-1}"

if [ $# -gt 0 ]; then
    CHROMS=("$@")
else
    CHROMS=()
    for i in $(seq 1 22); do CHROMS+=("chr$i"); done
fi

START=$(date +%s)
N=${#CHROMS[@]}
i=0
for CHROM in "${CHROMS[@]}"; do
    i=$((i + 1))
    echo ""
    echo "================================================================"
    echo "[H1] $CHROM  ($i / $N)"
    echo "================================================================"
    CHROM="$CHROM" bash "$REPO/experiments/h1_representation/run.sh"
done

ELAPSED=$(( $(date +%s) - START ))
echo ""
echo "=== H1 genome-wide complete in ${ELAPSED}s ==="
echo "Next: python experiments/h1_representation/aggregate.py"