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#include "btllib/seq_reader.hpp"
#include "btllib/util.hpp"
#include "helpers.hpp"
#include <fstream>
#include <iostream>
int
main()
{
const char* ids[] = { "asdf", "ghjk" };
const char* seqs[] = { "ACTG", "TGCA" };
const char* quals[] = { "!@^&", "(#&$" };
std::string random_filename;
for (int iteration = 0; iteration < 3; iteration++) {
std::cerr << "Iteration " << iteration + 1 << std::endl;
std::cerr << "Test multiline FASTQ" << std::endl;
btllib::SeqReader reader(btllib::get_dirname(__FILE__) +
"/input_multiline.fq",
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(reader.get_format(), btllib::SeqReader::Format::FASTQ);
size_t i = 0;
for (const auto record : reader) {
TEST_ASSERT_EQ(record.id, ids[i]);
TEST_ASSERT_EQ(record.seq, seqs[i]);
TEST_ASSERT_EQ(record.qual, quals[i]);
i++;
}
TEST_ASSERT_EQ(i, 2);
reader.close();
std::cerr << "Test random multiline FASTQ file" << std::endl;
std::vector<std::string> generated_ids;
std::vector<std::string> generated_comments;
std::vector<std::string> generated_seqs;
std::vector<std::string> generated_quals;
random_filename = get_random_name(64);
std::ofstream random_seqs_multiline(random_filename);
for (int s = 0; s < 500; s++) {
std::string id, comment_spaces, comment, seq, qual;
id = get_random_name(10);
comment_spaces = std::string(get_random(1, 10), ' ');
comment = get_random_name(20);
size_t seq_size = get_random(100, 2000);
seq = get_random_seq(seq_size);
qual = get_random_name(seq_size);
std::string seq_multiline = split_seq_multiline(seq);
std::string qual_multiline = split_seq_multiline(qual);
std::string newline = get_random(0, 1) == 1 ? "\r\n" : "\n";
random_seqs_multiline << '@' << id << ' ' << comment << newline
<< seq_multiline << newline << '+' << newline
<< qual_multiline << newline;
generated_ids.push_back(id);
generated_comments.push_back(comment);
generated_seqs.push_back(seq);
generated_quals.push_back(qual);
}
random_seqs_multiline.close();
std::cerr << random_filename << std::endl;
btllib::SeqReader random_reader(random_filename,
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(random_reader.get_format(),
btllib::SeqReader::Format::FASTQ);
btllib::SeqReader::Record record;
for (i = 0; (record = random_reader.read()); i++) {
TEST_ASSERT_EQ(record.id, generated_ids[i]);
TEST_ASSERT_EQ(record.comment, generated_comments[i]);
TEST_ASSERT_EQ(record.seq, generated_seqs[i]);
TEST_ASSERT_EQ(record.qual, generated_quals[i]);
}
TEST_ASSERT_EQ(i, 500);
random_reader.close();
std::remove(random_filename.c_str());
}
return 0;
}
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