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/*
* =====================================================================================
*
* Filename: SAMHeaderPrinter_gtest.cpp
*
* Description: Test alignment/format/SAMHeaderPrinter.hpp
*
* Version: 1.0
* Created: 03/24/2015 04:51:29 PM
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <algorithm>
#include <cstdio>
#include <cstring>
#include <string>
#include <vector>
#include <gtest/gtest.h>
#define private public
#define protected public
#include <alignment/format/SAMPrinter.hpp>
TEST(SAMPrinterTest, AddMatchBlockCigarOps)
{
DNASequence qSeq;
qSeq.Copy("XXXXXAAAAAGGGGGCCCCC");
DNASequence tSeq;
tSeq.Copy("AAAAANGGGGCCCCC");
blasr::Block b;
b.qPos = 5;
b.tPos = 0;
b.length = 15;
std::vector<int> opSize;
std::vector<char> opChar;
DNALength qSeqPos = 0;
DNALength tSeqPos = 0;
const std::vector<int> expOpSize = {5, 1, 9};
const std::vector<char> expOpChar = {'=', 'X', '='};
AddMatchBlockCigarOps(qSeq, tSeq, b, qSeqPos, tSeqPos, opSize, opChar);
EXPECT_EQ(opSize, expOpSize);
EXPECT_EQ(opChar, expOpChar);
}
std::string merge_indels(const std::vector<int>& opSize, const std::vector<char>& opChar)
{
std::vector<int> opSize_ = opSize;
std::vector<char> opChar_ = opChar;
SAMOutput::MergeAdjacentIndels(opSize_, opChar_, 'X');
std::string ret = "";
SAMOutput::CigarOpsToString(opSize_, opChar_, ret);
return ret;
}
TEST(SAMPrinterTest, MergeAdjacentIndels)
{
std::vector<int> opSize({10, 1, 5, 7, 6});
std::vector<char> opChar({'=', '=', '=', 'X', 'X'});
EXPECT_EQ(merge_indels(opSize, opChar), "16=13X");
opChar = std::vector<char>({'I', 'D', 'D', '=', 'I'});
EXPECT_EQ(merge_indels(opSize, opChar), "6X4I7=6I");
opChar = std::vector<char>({'I', 'D', 'D', 'I', 'I'});
EXPECT_EQ(merge_indels(opSize, opChar), "6X17I");
opChar = std::vector<char>({'=', 'D', 'D', 'I', 'I'});
EXPECT_EQ(merge_indels(opSize, opChar), "10=6X7I");
opChar = std::vector<char>({'I', 'D', '=', 'I', 'D'});
EXPECT_EQ(merge_indels(opSize, opChar), "1X9I5=6X1I");
opSize = std::vector<int>({1, 1});
opChar = std::vector<char>({'I', 'D'});
EXPECT_EQ(merge_indels(opSize, opChar), "1X");
opSize = std::vector<int>({1, 10});
opChar = std::vector<char>({'I', 'D'});
EXPECT_EQ(merge_indels(opSize, opChar), "1X9D");
opSize = std::vector<int>({1});
opChar = std::vector<char>({'='});
EXPECT_EQ(merge_indels(opSize, opChar), "1=");
opSize = std::vector<int>({1});
opChar = std::vector<char>({'I'});
EXPECT_EQ(merge_indels(opSize, opChar), "1I");
opSize = std::vector<int>({1, 10});
opChar = std::vector<char>({'X', '='});
EXPECT_EQ(merge_indels(opSize, opChar), "1X10=");
opSize = std::vector<int>({1, 10});
opChar = std::vector<char>({'I', '='});
EXPECT_EQ(merge_indels(opSize, opChar), "1I10=");
}
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