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/*
* =====================================================================================
*
* Filename: NucConversion_gtest.cpp
*
* Description: Test pbdata/NucConversion.hpp
*
* Version: 1.0
* Created: 08/19/2014 05:21:12 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <gtest/gtest.h>
#include <pbdata/NucConversion.hpp>
// ACGT = 0123
TEST(NucConversion, ASCIITo2BIT)
{
EXPECT_EQ(TwoBit[static_cast<size_t>('A')], 0);
EXPECT_EQ(TwoBit[static_cast<size_t>('a')], 0);
EXPECT_EQ(TwoBit[static_cast<size_t>('C')], 1);
EXPECT_EQ(TwoBit[static_cast<size_t>('c')], 1);
EXPECT_EQ(TwoBit[static_cast<size_t>('G')], 2);
EXPECT_EQ(TwoBit[static_cast<size_t>('g')], 2);
EXPECT_EQ(TwoBit[static_cast<size_t>('T')], 3);
EXPECT_EQ(TwoBit[static_cast<size_t>('t')], 3);
EXPECT_EQ(TwoBit[static_cast<size_t>('N')], 255);
EXPECT_EQ(TwoBit[static_cast<size_t>('x')], 255);
}
TEST(NucConversion, ASCIITo3BIT)
{
EXPECT_EQ(ThreeBit[static_cast<size_t>('A')], 0);
EXPECT_EQ(ThreeBit[static_cast<size_t>('a')], 0);
EXPECT_EQ(ThreeBit[static_cast<size_t>('C')], 1);
EXPECT_EQ(ThreeBit[static_cast<size_t>('c')], 1);
EXPECT_EQ(ThreeBit[static_cast<size_t>('G')], 2);
EXPECT_EQ(ThreeBit[static_cast<size_t>('g')], 2);
EXPECT_EQ(ThreeBit[static_cast<size_t>('T')], 3);
EXPECT_EQ(ThreeBit[static_cast<size_t>('t')], 3);
EXPECT_EQ(ThreeBit[static_cast<size_t>('U')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('M')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('R')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('W')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('S')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('Y')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('K')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('V')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('H')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('D')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('N')], 4);
EXPECT_EQ(ThreeBit[static_cast<size_t>('$')], 5);
EXPECT_EQ(ThreeBit[static_cast<size_t>('p')], 255);
EXPECT_EQ(ThreeBit[static_cast<size_t>('q')], 255);
}
TEST(NucConversion, ISACTG)
{
EXPECT_TRUE(IsACTG[static_cast<size_t>('A')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('a')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('C')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('c')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('G')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('g')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('T')]);
EXPECT_TRUE(IsACTG[static_cast<size_t>('t')]);
EXPECT_FALSE(IsACTG[static_cast<size_t>('w')]);
EXPECT_FALSE(IsACTG[static_cast<size_t>('N')]);
}
TEST(NucConversion, ThreeBitToASCII)
{
char alphabeta[] = {'A', 'C', 'G', 'T'};
for (int i = 0; i < 4; i++) {
EXPECT_EQ(alphabeta[i], ThreeBitToAscii[ThreeBit[static_cast<size_t>(alphabeta[i])]]);
}
}
TEST(NucConversion, AllToUpper)
{
char alphabeta[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'};
for (int i = 0; i < 8; i++) {
EXPECT_EQ(toupper(alphabeta[i]), AllToUpper[static_cast<size_t>(alphabeta[i])]);
}
}
TEST(NucConversion, AllToLower)
{
char alphabeta[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'};
for (int i = 0; i < 8; i++) {
EXPECT_EQ(tolower(alphabeta[i]), AllToLower[static_cast<size_t>(alphabeta[i])]);
}
}
TEST(NucConversion, ReverseComplementNuc)
{
EXPECT_EQ(ReverseComplementNuc[static_cast<size_t>('A')], 'T');
EXPECT_EQ(ReverseComplementNuc[static_cast<size_t>('T')], 'A');
EXPECT_EQ(ReverseComplementNuc[static_cast<size_t>('G')], 'C');
EXPECT_EQ(ReverseComplementNuc[static_cast<size_t>('C')], 'G');
}
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