int main()
{
int i, digit;
pnode phead = NULL;
init_node(&phead, sizeof(snode));
create_chain(phead);
pnode arr[N];
for (i = 0; i < N; i++) {
init_node(&arr[i], sizeof(snode));
}
digit = max_digit(phead);
for (i = 0; i < digit; i++) {
phead_to_arr(phead, arr);
arr_to_phead(phead, arr);
}
show_chain(phead);
for (i = 0; i < N; i++) {
destroy_chain(&arr[i]);
}
destroy_chain(&phead);
return 0;
}
int main()
{
pnode phead = NULL;
init_node(&phead, sizeof(snode));
create_chain(phead);
show_chain(phead);
destroy_chain(&phead);
return 0;
}
void cleanup(void)
{
PUTS("cleanup");
hotkey_t *hk = hotkeys_head;
while (hk != NULL) {
hotkey_t *next = hk->next;
destroy_chain(hk->chain);
free(hk->cycle);
free(hk);
hk = next;
}
hotkeys_head = hotkeys_tail = NULL;
}
static void consensus(args_t *args)
{
htsFile *fasta = hts_open(args->ref_fname, "rb");
if ( !fasta ) error("Error reading %s\n", args->ref_fname);
kstring_t str = {0,0,0};
while ( hts_getline(fasta, KS_SEP_LINE, &str) > 0 )
{
if ( str.s[0]=='>' )
{
// new sequence encountered, apply all chached variants
while ( args->vcf_rbuf.n )
{
if (args->chain) {
print_chain(args);
destroy_chain(args);
}
bcf1_t *rec = args->vcf_buf[args->vcf_rbuf.f];
if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) break;
int i = rbuf_shift(&args->vcf_rbuf);
apply_variant(args, args->vcf_buf[i]);
}
flush_fa_buffer(args, 0);
init_region(args, str.s+1);
continue;
}
args->fa_length += str.l;
args->fa_src_pos += str.l;
// determine if uppercase or lowercase is used in this fasta file
if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0;
if ( args->mask && args->rid>=0) mask_region(args, str.s, str.l);
kputs(str.s, &args->fa_buf);
bcf1_t **rec_ptr = NULL;
while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
{
bcf1_t *rec = *rec_ptr;
// still the same chr and the same region? if not, fasta buf can be flushed
if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) )
{
// save the vcf record until next time and flush
unread_vcf_line(args, rec_ptr);
rec_ptr = NULL;
break;
}
// is the vcf record well beyond cached fasta buffer? if yes, the buf can be flushed
if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos )
{
unread_vcf_line(args, rec_ptr);
rec_ptr = NULL;
break;
}
// is the cached fasta buffer full enough? if not, read more fasta, no flushing
if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen )
{
unread_vcf_line(args, rec_ptr);
break;
}
apply_variant(args, rec);
}
if ( !rec_ptr ) flush_fa_buffer(args, 60);
}
if (args->chain) {
print_chain(args);
destroy_chain(args);
}
flush_fa_buffer(args, 0);
hts_close(fasta);
free(str.s);
}
/**
* Destroy the RNA
*/
RNA::~RNA() {
destroy_chain();
if (m_destroy_trna == 1)
delete[] m_trna;
}
/**
* Set a new RNA chain
*/
void RNA::set_chain(CodonNode *chain) {
destroy_chain();
m_chain = chain;
}
