void
test_io_stream_open
(void)
{
iostream_t * stream;
// Test invalid arguments.
redirect_stderr();
stream = io_stream_open("fake-file.txt");
test_assert(stream == NULL);
unredirect_stderr();
// Load files.
stream = io_stream_open("examples/io_input.raw");
test_assert(stream != NULL);
io_stream_free(stream);
stream = io_stream_open("examples/io_input.fasta");
test_assert(stream != NULL);
io_stream_free(stream);
stream = io_stream_open("examples/io_input.fastq");
test_assert(stream != NULL);
io_stream_free(stream);
}
void i_stream_unref(struct istream **stream)
{
struct istream_private *_stream = (*stream)->real_stream;
if (_stream->iostream.refcount == 1) {
if (_stream->line_str != NULL)
str_free(&_stream->line_str);
}
if (!io_stream_unref(&(*stream)->real_stream->iostream)) {
if ((*stream)->real_stream->parent != NULL)
i_stream_unref(&(*stream)->real_stream->parent);
io_stream_free(&(*stream)->real_stream->iostream);
}
*stream = NULL;
}
void
test_io_stream_read_seq
(void)
{
iostream_t * stream;
gstack_t * stack;
seqread_t * read;
// Invalid arguments.
redirect_stderr();
test_assert(io_stream_read_seq(NULL) == NULL);
unredirect_stderr();
// Load files.
// Read RAW file.
stream = io_stream_open("examples/io_input.raw");
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 6);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNLLYYYYJDFLS") == 0);
test_assert(strcmp(seqread_tag(read), "6") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNNNACGTACGCC") == 0);
test_assert(strcmp(seqread_tag(read), "5") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ACGTACATGTATGACAC") == 0);
test_assert(strcmp(seqread_tag(read), "4") == 0);
seqread_free(read);
gstack_free(stack);
io_stream_free(stream);
// Read FASTA file.
stream = io_stream_open_buf("examples/io_input.fasta", 80);
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 4);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ACGTACATGTATGACAC") == 0);
test_assert(strcmp(seqread_tag(read), "seq4") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "AGTCGANTATACNTACG") == 0);
test_assert(strcmp(seqread_tag(read), "seq3") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "GTATCGACTACGAGCTA") == 0);
test_assert(strcmp(seqread_tag(read), "seq2") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ATGCGTACGTCGTATCA") == 0);
test_assert(strcmp(seqread_tag(read), "seq1") == 0);
seqread_free(read);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNLLYYYYJDFLS") == 0);
test_assert(strcmp(seqread_tag(read), "seq6") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNNNACGTACGCC") == 0);
test_assert(strcmp(seqread_tag(read), "seq5") == 0);
seqread_free(read);
gstack_free(stack);
io_stream_free(stream);
// Read FASTQ file.
stream = io_stream_open_buf("examples/io_input.fastq", 50);
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "GTATCGACTACGAGCTA") == 0);
test_assert(strcmp(seqread_tag(read), "seq2") == 0);
test_assert(strcmp(seqread_qscore(read), "BACBABCA0ACBB00AC") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ATGCGTACGTCGTATCA") == 0);
test_assert(strcmp(seqread_tag(read), "seq1") == 0);
test_assert(strcmp(seqread_qscore(read), "12391284194819241") == 0);
seqread_free(read);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 0);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert(stack == NULL);
io_stream_free(stream);
}
