#!/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 "Align from FASTA->FASTA"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.fasta --preserve-order --realign --db $T/extracted.arb"
assert_output_contains "align 12 sequences"
assert_exit_success
end_test

begin_test "Align from FASTA->FASTA(stdout)"
capture_stdouterr "$SINA -i $T/extracted.fasta --preserve-order --realign --db $T/extracted.arb >$T/aligned.2.fasta"
assert_output_contains "align 12 sequences"
assert_exit_success
capture_stdouterr "cmp $T/aligned.fasta $T/aligned.2.fasta"
assert_exit_success
end_test

begin_test "Align from FASTA->ARB"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.arb --realign --db $T/extracted.arb"
assert_output_contains "align 12 sequences"
assert_exit_success
end_test

begin_test "Align from ARB->ARB"
capture_stdouterr "$SINA -i $T/extracted.arb -o $T/aligned.arb --realign --db $T/extracted.arb"
assert_output_contains "align 12 sequences"
assert_exit_success
end_test

begin_test "Add relatives FASTA->FASTA"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.fasta --add-relatives 2 --db $T/ref.arb -v"
assert_output_contains "align 12 sequences"
assert_output_contains "wrote 36 sequences (0 excluded, 24 relatives)"
end_test

begin_test "Add relatives FASTA->ARB"
capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.arb --add-relatives 2 --db $T/ref.arb -v"
assert_output_contains "align 12 sequences"
assert_output_contains "wrote 36 sequences (0 excluded, 24 relatives)"
end_test