#! /bin/bash

FS_LR=7

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <reliable_seq> <less_reliable_seq> <stem>"
    echo "Perform MACSE alignment on given sequences"
    exit 1
fi

seq=$1
seq_lr=$2
stem=$3

{
    echo "Command:"
    echo "macse -prog alignSequences -seq $seq -seq_lr ${seq_lr}"
    echo "      -out_NT ${stem}.nal -out_AA ${stem}.pal"
    echo "      -optim 2 -max_refine_iter 3 -local_realign_init 0.2 -fs_lr $FS_LR"
} >alignSequences.log
macse -prog alignSequences \
    -seq "$seq" -seq_lr "${seq_lr}" \
    -out_NT "$stem".nal -out_AA "$stem".pal \
    -optim 2 \
    -max_refine_iter 3 \
    -local_realign_init 0.2 \
    -fs_lr $FS_LR \
    >>alignSequences.log 2>&1