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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;
size_t i;
btllib::SeqReader::Record record;
std::cerr << "Test small FASTA and FASTQ simultaneously" << std::endl;
btllib::SeqReader reader_fasta(btllib::get_dirname(__FILE__) +
"/input.fa.gz.bz2.xz",
btllib::SeqReader::Flag::SHORT_MODE);
btllib::SeqReader reader_fastq(btllib::get_dirname(__FILE__) +
"/input.fq.tar.xz",
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(reader_fasta.get_format(), btllib::SeqReader::Format::FASTA);
TEST_ASSERT_EQ(reader_fastq.get_format(), btllib::SeqReader::Format::FASTQ);
i = 0;
bool success_fasta = false, success_fastq = false;
for (;;) {
if ((success_fasta = (record = reader_fasta.read()))) {
TEST_ASSERT_EQ(record.id, ids[i]);
TEST_ASSERT_EQ(record.seq, seqs[i]);
TEST_ASSERT(record.qual.empty());
}
if ((success_fastq = (record = reader_fastq.read()))) {
TEST_ASSERT_EQ(record.id, ids[i]);
TEST_ASSERT_EQ(record.seq, seqs[i]);
TEST_ASSERT_EQ(record.qual, quals[i]);
}
if (++i == 3) {
TEST_ASSERT(success_fasta == false && success_fastq == false);
break;
} else {
TEST_ASSERT(success_fasta == true && success_fastq == true);
}
}
std::cerr << "Test larger randomly generated 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(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 newline = get_random(0, 1) == 1 ? "\r\n" : "\n";
random_seqs << '@' << id << comment_spaces << comment << newline << seq
<< newline << '+' << newline << qual << newline;
generated_ids.push_back(id);
generated_comments.push_back(comment);
generated_seqs.push_back(seq);
generated_quals.push_back(qual);
}
random_seqs.close();
btllib::SeqReader random_reader(random_filename,
btllib::SeqReader::Flag::LONG_MODE);
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::cerr << "Test larger randomly generated FASTQ file in parallel"
<< std::endl;
std::vector<long> read_nums;
std::vector<std::string> parallel_ids;
std::vector<std::string> parallel_comments;
std::vector<std::string> parallel_seqs;
std::vector<std::string> parallel_quals;
btllib::SeqReader random_reader2(random_filename,
btllib::SeqReader::Flag::LONG_MODE);
#pragma omp parallel private(record) shared(random_reader2)
{
while ((record = random_reader2.read())) {
#pragma omp critical
{
read_nums.push_back(record.num);
parallel_ids.push_back(record.id);
parallel_comments.push_back(record.comment);
parallel_seqs.push_back(record.seq);
parallel_quals.push_back(record.qual);
}
}
}
std::sort(read_nums.begin(), read_nums.end());
std::sort(generated_ids.begin(), generated_ids.end());
std::sort(generated_comments.begin(), generated_comments.end());
std::sort(generated_seqs.begin(), generated_seqs.end());
std::sort(generated_quals.begin(), generated_quals.end());
std::sort(parallel_ids.begin(), parallel_ids.end());
std::sort(parallel_comments.begin(), parallel_comments.end());
std::sort(parallel_seqs.begin(), parallel_seqs.end());
std::sort(parallel_quals.begin(), parallel_quals.end());
for (i = 0; i < parallel_ids.size(); i++) {
TEST_ASSERT_EQ(read_nums[i], long(i));
TEST_ASSERT_EQ(parallel_ids[i], generated_ids[i]);
TEST_ASSERT_EQ(parallel_comments[i], generated_comments[i]);
TEST_ASSERT_EQ(parallel_seqs[i], generated_seqs[i]);
TEST_ASSERT_EQ(parallel_quals[i], generated_quals[i]);
}
TEST_ASSERT_EQ(i, 500);
TEST_ASSERT_EQ(size_t(i), read_nums.size());
std::cerr << "Test larger randomly generated FASTQ file in parallel "
"(different syntax)"
<< std::endl;
read_nums.clear();
parallel_ids.clear();
parallel_comments.clear();
parallel_seqs.clear();
parallel_quals.clear();
btllib::SeqReader random_reader3(random_filename,
btllib::SeqReader::Flag::LONG_MODE);
#pragma omp parallel shared(read_nums, \
parallel_ids, \
parallel_comments, \
parallel_seqs, \
parallel_quals, \
random_reader3)
for (const auto record : random_reader3) {
#pragma omp critical
{
read_nums.push_back(record.num);
parallel_ids.push_back(record.id);
parallel_comments.push_back(record.comment);
parallel_seqs.push_back(record.seq);
parallel_quals.push_back(record.qual);
}
}
std::sort(read_nums.begin(), read_nums.end());
std::sort(parallel_ids.begin(), parallel_ids.end());
std::sort(parallel_comments.begin(), parallel_comments.end());
std::sort(parallel_seqs.begin(), parallel_seqs.end());
std::sort(parallel_quals.begin(), parallel_quals.end());
for (i = 0; i < parallel_ids.size(); i++) {
TEST_ASSERT_EQ(read_nums[i], long(i));
TEST_ASSERT_EQ(parallel_ids[i], generated_ids[i]);
TEST_ASSERT_EQ(parallel_comments[i], generated_comments[i]);
TEST_ASSERT_EQ(parallel_seqs[i], generated_seqs[i]);
TEST_ASSERT_EQ(parallel_quals[i], generated_quals[i]);
}
TEST_ASSERT_EQ(i, 500);
TEST_ASSERT_EQ(size_t(i), read_nums.size());
std::cerr << "Test larger randomly generated FASTQ file with read_block"
<< std::endl;
read_nums.clear();
parallel_ids.clear();
parallel_comments.clear();
parallel_seqs.clear();
parallel_quals.clear();
btllib::SeqReader random_reader4(random_filename,
btllib::SeqReader::Flag::LONG_MODE);
#pragma omp parallel shared(read_nums, \
parallel_ids, \
parallel_comments, \
parallel_seqs, \
parallel_quals, \
random_reader4)
while (true) {
auto block = random_reader4.read_block();
if (block.count == 0) {
break;
}
for (auto record : block.data) {
#pragma omp critical
{
read_nums.push_back(record.num);
parallel_ids.push_back(record.id);
parallel_comments.push_back(record.comment);
parallel_seqs.push_back(record.seq);
parallel_quals.push_back(record.qual);
}
}
}
std::sort(read_nums.begin(), read_nums.end());
std::sort(parallel_ids.begin(), parallel_ids.end());
std::sort(parallel_comments.begin(), parallel_comments.end());
std::sort(parallel_seqs.begin(), parallel_seqs.end());
std::sort(parallel_quals.begin(), parallel_quals.end());
for (i = 0; i < parallel_ids.size(); i++) {
TEST_ASSERT_EQ(read_nums[i], long(i));
TEST_ASSERT_EQ(parallel_ids[i], generated_ids[i]);
TEST_ASSERT_EQ(parallel_comments[i], generated_comments[i]);
TEST_ASSERT_EQ(parallel_seqs[i], generated_seqs[i]);
TEST_ASSERT_EQ(parallel_quals[i], generated_quals[i]);
}
TEST_ASSERT_EQ(i, 500);
TEST_ASSERT_EQ(size_t(i), read_nums.size());
std::remove(random_filename.c_str());
}
return 0;
}
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