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#include "btllib/seq_writer.hpp"
#include "btllib/seq_reader.hpp"
#include "helpers.hpp"
#include <cstdio>
#include <fstream>
int
main()
{
const char* ids[] = { "1", "2" };
const char* comments[] = { "comment1", "comment2" };
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;
// Test FASTA
random_filename = get_random_name(64);
std::cerr << "Test FASTA" << std::endl;
btllib::SeqWriter writer_fasta(random_filename, btllib::SeqWriter::FASTA);
for (int i = 0; i < 2; i++) {
writer_fasta.write(ids[i], comments[i], seqs[i], "");
}
writer_fasta.close();
btllib::SeqReader reader_fasta(random_filename,
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(reader_fasta.get_format(), btllib::SeqReader::Format::FASTA);
size_t i;
btllib::SeqReader::Record record;
i = 0;
while ((record = reader_fasta.read())) {
TEST_ASSERT_EQ(record.id, ids[i]);
TEST_ASSERT_EQ(record.comment, comments[i]);
TEST_ASSERT_EQ(record.seq, seqs[i]);
TEST_ASSERT(record.qual.empty());
i++;
}
TEST_ASSERT_EQ(i, 2);
reader_fasta.close();
std::remove(random_filename.c_str());
// Test FASTQ
random_filename = get_random_name(64) + ".bz2";
std::cerr << "Test FASTQ" << std::endl;
btllib::SeqWriter writer_fastq(random_filename, btllib::SeqWriter::FASTQ);
for (int j = 0; j < 2; j++) {
writer_fastq.write(ids[j], comments[j], seqs[j], quals[j]);
}
writer_fastq.close();
btllib::SeqReader reader_fastq(random_filename,
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(reader_fastq.get_format(), btllib::SeqReader::Format::FASTQ);
i = 0;
while ((record = reader_fastq.read())) {
TEST_ASSERT_EQ(record.id, ids[i]);
TEST_ASSERT_EQ(record.comment, comments[i]);
TEST_ASSERT_EQ(record.seq, seqs[i]);
TEST_ASSERT_EQ(record.qual, quals[i]);
i++;
}
TEST_ASSERT_EQ(i, 2);
reader_fastq.close();
std::remove(random_filename.c_str());
// Test larger randomly generated file
std::cerr << "Test random 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) + ".gz.xz.bz2";
btllib::SeqWriter random_seqs(
random_filename, btllib::SeqWriter::FASTQ, false);
for (int s = 0; s < 500; s++) {
std::string id, comment, seq, qual;
id = get_random_name(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);
random_seqs.write(id, comment, seq, qual);
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::remove(random_filename.c_str());
std::cerr << "Test random file in parallel" << std::endl;
auto generated_ids2 = generated_ids;
auto generated_comments2 = generated_comments;
auto generated_seqs2 = generated_seqs;
auto generated_quals2 = generated_quals;
auto random_filename2 = get_random_name(64) + ".gz";
btllib::SeqWriter random_seqs2(
random_filename2, btllib::SeqWriter::FASTQ, false);
#pragma omp parallel for shared(generated_ids2, \
generated_comments2, \
generated_seqs2, \
generated_quals2, \
random_seqs2)
for (int s = 0; s < 500; s++) {
std::string id, comment, seq, qual;
#pragma omp critical
{
id = generated_ids2.back();
generated_ids2.pop_back();
comment = generated_comments2.back();
generated_comments2.pop_back();
seq = generated_seqs2.back();
generated_seqs2.pop_back();
qual = generated_quals2.back();
generated_quals2.pop_back();
}
random_seqs2.write(id, comment, seq, qual);
}
random_seqs2.close();
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_filename2,
btllib::SeqReader::Flag::LONG_MODE);
while ((record = random_reader2.read())) {
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(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(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);
std::remove(random_filename2.c_str());
}
return 0;
}
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