#!/bin/bash
source tests/test_helper.sh

TEST_ARB=$TEST_ARGS
maketmpdir T

cp $TEST_ARB $T/ref.arb

SINA="./src/sina"

begin_test "PREP"
capture_stdouterr "$SINA -i $T/ref.arb -o $T/extracted.fasta --select-step 1000 --prealigned"
assert_exit_success
assert_output_contains "align 12 sequences"
capture_stdouterr "$SINA -i $T/ref.arb -o $T/extracted.arb --select-step 1000 --prealigned"
assert_exit_success
assert_output_contains "align 12 sequences"
end_test

begin_test "Search"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/results.fasta --db $T/ref.arb --prealigned --search -v"
assert_output_count "nearest_slv: \w" -eq 12
end_test

begin_test "Search - add relatives"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/results.fasta --db $T/ref.arb --prealigned --search -v --add-relatives 2"
assert_output_count "nearest_slv: \w" -eq 12
assert_output_contains "24 relatives"
end_test