#!/bin/bash -e

rm -f single* search_* blits_*

if $(command -v "ffindex_apply_mpi" >/dev/null 2>&1); then
    MPI=1
else
    unset MPI
fi

hhalign -i query.a3m -t query.a3m

ffindex_build -s single.ffdata single.ffindex query.a3m

APPLY="ffindex_apply"
if [ -n "$MPI" ]; then
    APPLY="mpirun -np 2 ffindex_apply_mpi"
fi

$APPLY single.ffdata single.ffindex -d single_a3m_cons.ffdata -i single_a3m_cons.ffindex \
        -- hhconsensus -i stdin -oa3m stdout -M a3m -v 0

$APPLY single_a3m_cons.ffdata single_a3m_cons.ffindex -d single_a3m.ffdata -i single_a3m.ffindex \
        -- hhfilter -i stdin -o stdout -diff 1000 -v 0

$APPLY single_a3m.ffdata single_a3m.ffindex -d single_hhm.ffdata -i single_hhm.ffindex \
        -- hhmake -i stdin -o stdout -v 0

if [ -n "$MPI" ]; then
    mpirun -np 2 cstranslate_mpi -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m
else
    cstranslate -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m -f
fi

hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
hhblits_omp -i single -d single -blasttab blits_omp_res -n 1
diff <(tr -d '\000' < blits_omp_res.ffdata) blits_app_res
if [ -n "$MPI" ]; then
    mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
    diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
fi

hhsearch -i query.a3m -d single -blasttab search_app_res
hhsearch_omp -i single -d single -blasttab search_omp_res
diff <(tr -d '\000' < search_omp_res.ffdata) search_app_res

if [ -n "$MPI" ]; then
    mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
    diff <(tr -d '\000' < search_mpi_res.ffdata) search_app_res
fi

diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)