void test_read_fasta_file(struct test *t) {
t_set_msg(t, "Testing reading a fasta File...");
struct genome_sequence *sequence_table = NULL;
char filename[30] = "test/data/test.fasta";
int err = read_fasta_file(&sequence_table, filename);
t_assert_msg(t, err == E_SUCCESS, "Parsing failed");
t_log(t, "Error: %d\n", err);
struct genome_sequence *s = NULL;
struct genome_sequence *tmp = NULL;
HASH_ITER(hh, sequence_table, s, tmp) {
s->data[s->n] = 0;
t_log(t, "%s %s \n\n", s->chrom, s->data);
}
file_desc *init_file_desc()
{
file_desc *f_desc = NULL;
t_lock *block_list_lock = NULL;
if(NULL == (f_desc = (file_desc *)t_malloc(sizeof(file_desc))))
{
t_log("malloc login_buf frame error!");
return NULL;
}
if(NULL == (f_desc->block_head =\
(file_block_desc *)t_malloc(sizeof(file_block_desc))))
return NULL;
f_desc->block_head->next = NULL;
f_desc->block_tail = f_desc->block_head;
block_list_lock = (t_lock *)t_malloc(sizeof(t_lock));
init_lock(block_list_lock);
f_desc->block_list_lock = block_list_lock;
f_desc->file_size = 0;
f_desc->file_id = 0;
f_desc->block_count = 0;
f_desc->last_frame_count = 0;
f_desc->frame_remain = NULL;
return f_desc;
}
void test_valid_line(struct test *t) {
t_set_msg(t, "Testing reading a valid Sam line...");
char sample_line[1000] =
"Seq23599_x1\t272\tscaffold_1\t67\t0\t"
"21M\t*\t0\t0\tGCCACCCATGCCGCATCCACA\t"
"IIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\t"
"XG:i:0\tNM:i:1\tMD:Z:12A8\tYT:Z:UU\tNH:i:16\tCC:Z:=\t"
"CP:i:250\tHI:i:0\n";
struct sam_entry *test_entry = NULL;
int result = parse_line(&test_entry, sample_line);
t_assert_msg(t, result == E_SUCCESS, "Parsing the line failed");
t_assert_msg(t, test_entry->flag == 272, "Flag parsed wrong");
t_assert_msg(t, test_entry->pos == 67, "Position parsed wrong");
t_log(t, "%s", test_entry->seq);
t_assert_msg(t, strcmp(test_entry->seq, "GCCACCCATGCCGCATCCACA") == 0,
"Sequence parsed wrong");
free_sam_entry(test_entry);
}
void read_thread(void *args)
{
transfer_session *session;
file_desc *f_desc;
file_block_desc *b_desc;
frame_index *f_index, *last_index;
FILE *fp = NULL;
int err;
int i = 0;
session = (transfer_session *)args;
f_desc = session->f_desc;
for(;;)
{
if(session->state != STATE_TRANSFER)
{
/* if state = finish, close file and exit the thread */
if(fp)
{
fclose(fp);
fp = NULL;
}
sleep(1);
continue;
}
if(NULL == fp)
{
if(NULL == (fp = fopen(f_desc->file_name, "r")))
{
t_log("open file error");
continue;
}
}
b_desc = get_first_block(f_desc);
if(b_desc == ERR_BLOCK_LIST_NULL)
return;
else if(b_desc == ERR_BLOCK_LIST_EMPTY)
{
sleep(1);
continue;
}
else
{
if(b_desc->retry_flag == ORIGIN_FRAME)
{
f_index = b_desc->index;
for(i = 1; i <= MAX_FRAME_COUNT; i++)
{
f_index->frame_index = i;
if(read_file_to_msg_q(f_index, f_desc, fp, session->data_qid) < 0)
break;
}
t_free(f_index);
}
else if(b_desc->retry_flag == RETRAN_FRAME)
{
printf("read_thread re tran\n");
f_index = b_desc->index;
if(f_index->frame_index == 0XFFFF)
{
for(i = 1; i <= MAX_FRAME_COUNT; i++)
{
f_index->frame_index = i;
read_file_to_msg_q(f_index, f_desc, fp, session->data_qid);
}
t_free(f_index);
}
else
{
do
{
read_file_to_msg_q(f_index, f_desc, fp, session->data_qid);
last_index = f_index;
f_index = f_index->next;
t_free(last_index);
}while(f_index);
}
}
}
t_free(b_desc);
// printf("block:%d\n", b_desc->index->block_index);
}
return;
}
