void
qes_seqfile_set_format (struct qes_seqfile *seqfile,
enum qes_seqfile_format format)
{
if (!qes_seqfile_ok(seqfile)) return;
seqfile->format = format;
}
ssize_t
qes_seqfile_write (struct qes_seqfile *seqfile, struct qes_seq *seq)
{
#define sf_putc_check(c) ret = QES_ZFPUTC(seqfile->qf->fp, c); \
if (ret != c) {return -2;} \
else res_len += 1; \
ret = 0
#define sf_puts_check(s) ret = QES_ZFPUTS(seqfile->qf->fp, s); \
if (ret < 0) {return -2;} \
else res_len += ret; \
ret = 0
int ret = 0;
ssize_t res_len = 0;
if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) {
return -2;
}
switch (seqfile->format) {
case FASTA_FMT:
sf_putc_check(FASTA_DELIM);
sf_puts_check(seq->name.str);
if (qes_seq_has_comment(seq)) {
sf_putc_check(' ');
sf_puts_check(seq->comment.str);
}
sf_putc_check('\n');
sf_puts_check(seq->seq.str);
sf_putc_check('\n');
break;
case FASTQ_FMT:
sf_putc_check(FASTQ_DELIM);
sf_puts_check(seq->name.str);
if (qes_seq_has_comment(seq)) {
sf_putc_check(' ');
sf_puts_check(seq->comment.str);
}
sf_putc_check('\n');
sf_puts_check(seq->seq.str);
sf_putc_check('\n');
if (qes_seq_has_qual(seq)) {
sf_putc_check('+');
sf_putc_check('\n');
sf_puts_check(seq->qual.str);
sf_putc_check('\n');
}
break;
case UNKNOWN_FMT:
default:
return -2;
break;
}
return res_len;
#undef sf_putc_check
#undef sf_puts_check
}
static void
test_qes_seqfile_destroy (void *ptr)
{
struct qes_seqfile *sf = NULL;
char *fname = NULL;
(void) ptr;
/* Test file opening for reading */
fname = find_data_file("test.fastq");
tt_assert(fname != NULL);
sf = qes_seqfile_create(fname, "r");
tt_ptr_op(sf, !=, NULL);
tt_assert(qes_seqfile_ok(sf));
qes_seqfile_destroy(sf);
tt_ptr_op(sf, ==, NULL);
tt_assert(!qes_seqfile_ok(sf));
end:
qes_seqfile_destroy(sf);
if (fname != NULL) free(fname);
}
enum qes_seqfile_format
qes_seqfile_guess_format (struct qes_seqfile *seqfile)
{
int first_char = '\0';
if (!qes_seqfile_ok(seqfile)) return UNKNOWN_FMT;
if (!qes_file_readable(seqfile->qf)) return UNKNOWN_FMT;
first_char = qes_file_peek(seqfile->qf);
switch (first_char) {
case FASTQ_DELIM:
seqfile->format = FASTQ_FMT;
return FASTQ_FMT;
break;
case FASTA_DELIM:
seqfile->format = FASTA_FMT;
return FASTA_FMT;
break;
default:
seqfile->format = UNKNOWN_FMT;
return UNKNOWN_FMT;
}
}
ssize_t
qes_seqfile_read (struct qes_seqfile *seqfile, struct qes_seq *seq)
{
if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) {
return -2;
}
if (seqfile->qf->eof) {
return EOF;
}
if (seqfile->format == FASTQ_FMT) {
return read_fastq_seqfile(seqfile, seq);
} else if (seqfile->format == FASTA_FMT) {
return read_fasta_seqfile(seqfile, seq);
}
/* If we reach here, bail out with an error */
qes_str_nullify(&seq->name);
qes_str_nullify(&seq->comment);
qes_str_nullify(&seq->seq);
qes_str_nullify(&seq->qual);
return -2;
}
