#!/bin/bash
THREADS=${THREADS:-12}
MIN_DSF=${MIN_DSF:-0.01}

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <mrbayes_output_dir> <mbsum_output_dir> <num_skip>"
    echo "Summarize MrBayes output using mbsum, skipping analyses with high DSF"
    exit 1
fi

mb_dir=$(readlink -f "$1")
mbsum_out_dir=$2
num_skip=$3

mkdir -p "$mbsum_out_dir"
echo -n "" >mbsum.skip.log
echo -n "" >mbsum.cmds
for i in "$mb_dir"/*/mrbayes.log; do
    og_dir=$(dirname "$i")
    base=$(basename "$og_dir")
    ## skip Average standard deviation of split frequencies > 0.01
    dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "$i" 2>/dev/null)
    if awk -v d="$dsf" -v min_dsf="$MIN_DSF" 'BEGIN{if (d >= min_dsf) exit 0; exit 1}'; then
        echo "Skipping ${base} due to high DSF: ${dsf}" >>mbsum.skip.log
        continue
    else
        echo "mbsum ${og_dir}/*.t -n $num_skip -o $mbsum_out_dir/${base}.in >> $og_dir/mbsum.log 2>&1" >>mbsum.cmds
    fi
done
xargs -t -P "$THREADS" -I cmd -a mbsum.cmds bash -c "cmd"
echo "Mbsum all done!"