/*=== FUNCTION ============================================================*
Name: test_qes_seqfile_write
Description: Tests the qes_seqfile_write function from qes_seqfile.c
*===========================================================================*/
static void
test_qes_seqfile_write (void *ptr)
{
struct qes_seq *seq = qes_seq_create();
size_t expt_bytes = 0;
ssize_t res = 0;
struct qes_seqfile *sf = NULL;
char *fname = NULL;
char *crc = NULL;
(void) ptr;
/* Make a seq to write */
qes_seq_fill_name(seq, "HWI-TEST", 8);
qes_seq_fill_comment(seq, "testseq 1 2 3", 13);
qes_seq_fill_seq(seq, "ACTCAATT", 8);
qes_seq_fill_qual(seq, "IIIIIIII", 8);
expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */
8 + 1 + 2 + 8 + 1; /* seq + '\n' + "+\n" + qual + '\n' */
/* Test with a FASTQ seqfile */
fname = get_writable_file();
tt_assert(fname != NULL);
sf = qes_seqfile_create(fname, "wT");
qes_seqfile_set_format(sf, FASTQ_FMT);
res = qes_seqfile_write(sf, seq);
tt_int_op(res, ==, expt_bytes);
qes_seqfile_destroy(sf); /* Has to happen here to flush it */
crc = crc32_file(fname);
tt_str_op(crc, ==, "d4665941");
clean_writable_file(fname);
free(crc);
fname = NULL;
crc = NULL;
/* Test with a FASTA seqfile */
expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */
8 + 1; /* seq + '\n'*/
fname = get_writable_file();
tt_assert(fname != NULL);
sf = qes_seqfile_create(fname, "wT");
qes_seqfile_set_format(sf, FASTA_FMT);
/* do the write */
res = qes_seqfile_write(sf, seq);
tt_int_op(res, ==, expt_bytes);
qes_seqfile_destroy(sf); /* Flush it */
crc = crc32_file(fname);
tt_str_op(crc, ==, "0a295c77");
clean_writable_file(fname);
fname = NULL;
/* Check with bad params that it returns -2 */
res = qes_seqfile_write(NULL, seq);
tt_int_op(res, ==, -2);
res = qes_seqfile_write(sf, NULL);
tt_int_op(res, ==, -2);
end:
qes_seqfile_destroy(sf);
qes_seq_destroy(seq);
if (fname != NULL) free(fname);
if (crc != NULL) free(crc);
}
inline int
qes_seq_fill(struct qes_seq *seqobj, const char *name, const char *comment,
const char *seq, const char *qual)
{
if (!qes_seq_ok(seqobj) || name == NULL || comment == NULL || seq == NULL \
|| qual == NULL) {
return 1;
}
if (qes_seq_fill_name(seqobj, name, strlen(name)) != 0) return 1;
if (qes_seq_fill_comment(seqobj, comment, strlen(comment)) != 0) return 1;
if (qes_seq_fill_seq(seqobj, seq, strlen(seq)) != 0) return 1;
if (qes_seq_fill_qual(seqobj, qual, strlen(qual)) != 0) return 1;
return 0;
}
/*******************************************************************************
* MAIN *
*******************************************************************************/
int
convert_main(int argc, char *argv[])
{
int c = 0;
bool fasta = true;
const char *filename = NULL;
/* Parse CLI options */
while ((c = getopt(argc, argv, convert_optstr)) >= 0) {
switch (c) {
case 'a':
fasta = true;
break;
case 'q':
fasta = false;
break;
case 'h':
convert_usage(stdout);
return EXIT_SUCCESS;
break;
case '?':
convert_usage(stderr);
return EXIT_FAILURE;
break;
}
}
if (optind >= argc) {
convert_usage(stderr);
return EXIT_FAILURE;
}
filename = argv[optind];
struct qes_seq *seq = qes_seq_create();
struct qes_seqfile *sf = qes_seqfile_create(filename, "r");
ssize_t res;
char *tmpqual = NULL;
size_t tmpqual_sz = 0;
while ((res = qes_seqfile_read(sf, seq)) > 0) {
if (fasta) {
qes_seq_print(seq, stdout, true, 0);
} else {
size_t seqlen = seq->seq.len;
if (seq->qual.len < seqlen) {
if (seqlen > tmpqual_sz) {
tmpqual_sz = seqlen + 1;
tmpqual = realloc(tmpqual, seqlen);
if (tmpqual == NULL) {
fputs("OUT OF MEM\n", stderr);
return EXIT_FAILURE;
}
}
memset(tmpqual, 'I', seqlen);
tmpqual[seqlen] = 0;
qes_seq_fill_qual(seq, tmpqual, seqlen);
}
qes_seq_print(seq, stdout, false, 0);
}
}
if (tmpqual) free(tmpqual);
qes_seqfile_destroy(sf);
qes_seq_destroy(seq);
return EXIT_SUCCESS;
}
