#! /bin/bash
set -e
THREADS=${THREADS:-12}
if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <nal_dir> <out_dir> <ext>"
    echo "Trim MACSE nucleotide alignments using trimal"
    exit 1
fi

nal_dir=$(readlink -f "$1")
out_dir=$(readlink -f "$2")
ext=$3

mkdir -p "$out_dir"
echo -n >trimal.cmds
for i in "$nal_dir"/*."$ext"; do
    j=$(basename "$i" ."$ext")
    echo "trimal -in $i -out $out_dir/${j}.trimed.fa -automated1 -resoverlap 0.5 -seqoverlap 50" >>trimal.cmds
done
xargs -t -P "$THREADS" -I cmd -a trimal.cmds bash -c "cmd"