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// Copyright (c) 2020 Robert Vaser
#include "biosoup/nucleic_acid.hpp"
#include <iostream>
#include "gtest/gtest.h"
std::atomic<std::uint32_t> biosoup::NucleicAcid::num_objects{0};
namespace biosoup {
namespace test {
TEST(BiosoupNucleicAcidTest, NucleotideError) {
try {
NucleicAcid s{"test", "EFIJLOPQUXZ"};
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[biosoup::NucleicAcid::NucleicAcid] error: not a nucleotide");
}
}
TEST(BiosoupNucleicAcidTest, Inflate) {
NucleicAcid s{"test", "AaAaCcCcGgGgTtTt------ACGTRYKMSWBDHVN-nvhdbwsmkyrtgca------tTtTgGgGcCcCaAaA"}; // NOLINT
EXPECT_EQ(s.deflated_data.size(), s.deflated_data.capacity());
EXPECT_EQ(0, s.Code(16));
EXPECT_EQ(1, s.Code(23));
EXPECT_EQ(2, s.Code(35));
EXPECT_EQ(3, s.Code(59));
EXPECT_EQ("AAAACCCCGGGGTTTTAAAAAAACGTATGCCACATGAAAGTACACCGTATGCAAAAAAATTTTGGGGCCCCAAAA", s.InflateData()); // NOLINT
EXPECT_EQ("TATGCCACATGAAAGTACACCGTAT", s.InflateData(25, 25));
EXPECT_EQ("TGAAAGT", s.InflateData(34, 7));
EXPECT_EQ("", s.InflateData(75, 42));
EXPECT_EQ("C", s.InflateData(29, 1));
EXPECT_EQ("G", s.InflateData(64, 1));
EXPECT_EQ("CCAAAA", s.InflateData(69));
}
TEST(BiosoupNucleicAcidTest, Quality) {
NucleicAcid s{
"test",
"ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC", // NOLINT
"!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~"}; // NOLINT
EXPECT_EQ(s.block_quality.size(), s.block_quality.capacity());
EXPECT_EQ(31, s.Score(42));
EXPECT_EQ(78, s.Score(84));
EXPECT_EQ("@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@oooooooooooooooooooooooooooooo", s.InflateQuality()); // NOLINT
EXPECT_EQ("@@@@@@@@@@@@@@@@", s.InflateQuality(0, 16));
EXPECT_EQ("@@oo", s.InflateQuality(62, 4));
EXPECT_EQ("@", s.InflateQuality(63, 1));
EXPECT_EQ("o", s.InflateQuality(64, 1));
EXPECT_EQ("o", s.InflateQuality(93));
EXPECT_EQ("ooo", s.InflateQuality(91, 20));
EXPECT_EQ("", s.InflateQuality(95));
}
TEST(BiosoupNucleicAcidTest, ReverseAndComplement) {
NucleicAcid s{
"test",
"ACGTACTGAGCTAGTCATCGATGCCAGTCATGCGATCGTACTAGCTGAGACTGATCGCATGCTAGTACGTCA", // NOLINT
"0123456789012345678901234567890123456789012345678901234567890123ZZZZZZZZ"}; // NOLINT
NucleicAcid c{s};
c.ReverseAndComplement();
EXPECT_EQ("TGACGTACTAGCATGCGATCAGTCTCAGCTAGTACGATCGCATGACTGGCATCGATGACTAGCTCAGTACGT", c.InflateData()); // NOLINT
EXPECT_EQ("ZZZZZZZZ4444444444444444444444444444444444444444444444444444444444444444", c.InflateQuality()); // NOLINT
c.ReverseAndComplement();
EXPECT_EQ(c.InflateData(), s.InflateData());
EXPECT_EQ(c.InflateQuality(), s.InflateQuality());
}
} // namespace test
} // namespace biosoup
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