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

TEST_ARB=$TEST_ARGS
maketmpdir T

cp $TEST_ARB $T/ref.arb

SINA="./src/sina $SINA_EXTRA_PARAMS"

SINA="$SINA -i $T/ref.arb --db $T/ref.arb  --orig-db $T/ref.arb -o /dev/null --show-dist"
SINA="$SINA --threads 10 --fs-engine internal"

begin_test "prealigned"
capture_stdouterr "$SINA --select-step 250 --prealigned"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_contains "avg_sps: 1"
assert_output_contains "avg_cpm: 0"
assert_output_contains "avg_idty: 0"
end_test


begin_test "align copy"
capture_stdouterr "$SINA --select-step 1000"
assert_exit_success
assert_output_contains "align 12 sequences"
assert_output_contains "avg_sps: 1"
assert_output_contains "avg_cpm: 0"
assert_output_contains "avg_idty: 1"
end_test

begin_test "realign"
capture_stdouterr "$SINA --select-step 250 --realign"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.996"
assert_output_value avg_cpm: "<0.0002"
assert_output_value avg_idty: ">0.96"
end_test

begin_test "realign/noquery"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.996"
assert_output_value avg_cpm: "<0.00025"
assert_output_value avg_idty: ">0.96"
end_test

begin_test "realign/noquery k=8"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-len 8"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.996"
assert_output_value avg_cpm: "<0.0002"
assert_output_value avg_idty: ">0.96"
end_test

begin_test "realign/noquery nofast"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-no-fast"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.996"
assert_output_value avg_cpm: "<0.00015"
assert_output_value avg_idty: ">0.96"
end_test

begin_test "realign msc 0.9"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.9"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.99"
assert_output_value avg_cpm: "<0.001"
assert_output_value avg_idty: ">0.88" "<0.9"
end_test

begin_test "realign msc 0.8"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.8"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.97"
assert_output_value avg_cpm: "<0.002"
assert_output_value avg_idty: ">0.78" "<0.8"
end_test

begin_test "realign msc 0.7"
capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.7"
assert_exit_success
assert_output_contains "align 48 sequences"
assert_output_value avg_sps: ">0.95"
assert_output_value avg_cpm: "<0.01"
assert_output_value avg_idty: ">0.68" "<0.7"
end_test