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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[] = { "q1", "q2" };
const char* seqs[] = { "ACTG", "TGCA" };
const char* quals[] = { "!@^&", "(#&$" };
for (int iteration = 0; iteration < 3; iteration++) {
std::cerr << "Iteration " << iteration + 1 << std::endl;
std::cerr << "Test small SAM" << std::endl;
btllib::SeqReader reader(btllib::get_dirname(__FILE__) + "/input.bam",
btllib::SeqReader::Flag::SHORT_MODE);
TEST_ASSERT_EQ(reader.get_format(), btllib::SeqReader::Format::SAM);
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++;
}
std::cerr << "Test larger SAM file" << std::endl;
btllib::SeqReader large_fastq_reader(btllib::get_dirname(__FILE__) +
"/large.fq",
btllib::SeqReader::Flag::SHORT_MODE);
btllib::SeqReader large_bam_reader(btllib::get_dirname(__FILE__) +
"/large.bam",
btllib::SeqReader::Flag::SHORT_MODE);
while (true) {
btllib::SeqReader::Record record1 = large_fastq_reader.read();
btllib::SeqReader::Record record2 = large_bam_reader.read();
if (!bool(record1) && !bool(record2)) {
break;
}
TEST_ASSERT(record1)
TEST_ASSERT(record2)
TEST_ASSERT_EQ(record1.id, record2.id);
TEST_ASSERT_EQ(record1.comment, record2.comment);
TEST_ASSERT_EQ(record1.seq, record2.seq);
TEST_ASSERT_EQ(record1.qual, record2.qual);
}
}
return 0;
}
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