static void update_sub_window(void)
{
BUG_ON(!cur);
if (win[cur].menu_valign == TOP) {
int max_y0 = screen_height - win[cur].menu_height;
win[cur].menu_y0 = win[cur - 1].menu_y0 +
win[cur - 1].parent_item.y -
item_margin_y -
sub_padding_top;
if (win[cur].menu_y0 > max_y0)
win[cur].menu_y0 = max_y0;
} else if (win[cur].menu_valign == BOTTOM) {
win[cur].menu_y0 = win[cur - 1].menu_y0 +
win[cur - 1].parent_item.y +
win[cur - 1].parent_item.h +
item_margin_y +
sub_padding_bottom -
win[cur].menu_height;
if (win[cur].menu_y0 < screen_y0)
win[cur].menu_y0 = screen_y0;
}
if (win[cur].menu_halign == LEFT) {
left_align();
if (screen_x0 + screen_width - win[cur].menu_width <
win[cur].menu_x0)
right_align_and_adjust();
} else if (win[cur].menu_halign == RIGHT) {
right_align();
if (screen_x0 > win[cur].menu_x0)
left_align_and_adjust();
}
}
static void left_align_and_adjust(void)
{
int max_x0 = screen_x0 + screen_width - win[cur].menu_width;
left_align();
if (win[cur].menu_x0 > max_x0)
win[cur].menu_x0 = max_x0;
}
/**
* Extract reference sequence region for motif discovery.
*
* The input is a VCF record that contains an indel.
*
* If the the indel has multiple alleles, it will examine all
* alleles.
*
* todo: is might be a good idea to combine this step with motif detection
* since there seems to be a need to have an iterative process here
* to ensure a good candidate motif is chosen. *
*/
void CandidateRegionExtractor::extract_regions_by_exact_alignment(bcf_hdr_t* h, bcf1_t* v, Variant& variant)
{
if (debug)
{
if (debug) std::cerr << "********************************************\n";
std::cerr << "EXTRACTIING REGION BY EXACT LEFT AND RIGHT ALIGNMENT\n\n";
}
VNTR& vntr = variant.vntr;
const char* chrom = bcf_get_chrom(h, v);
int32_t min_beg1 = bcf_get_pos1(v);
int32_t max_end1 = min_beg1;
if (debug)
{
bcf_print_liten(h, v);
}
//merge candidate search region
for (size_t i=1; i<bcf_get_n_allele(v); ++i)
{
std::string ref(bcf_get_alt(v, 0));
std::string alt(bcf_get_alt(v, i));
int32_t pos1 = bcf_get_pos1(v);
//this prevents introduction of flanks that do not harbour the repeat unit
trim(pos1, ref, alt);
int32_t end1 = pos1 + ref.size() - 1;
right_align(chrom, end1, ref, alt);
int32_t beg1 = end1 - ref.size() + 1;
left_align(chrom, beg1, ref, alt);
min_beg1 = beg1<min_beg1 ? beg1 : min_beg1;
max_end1 = end1>max_end1 ? end1 : max_end1;
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "EXACT REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") from " << pos1 << ":" << ref << ":" << alt << "\n";
std::cerr << " " << seq << "\n";
}
if (seq_len) free(seq);
}
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "FINAL EXACT REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") " << "\n";
std::cerr << " " << seq << "\n";
}
vntr.exact_repeat_tract = seq;
vntr.rid = bcf_get_rid(v);
vntr.exact_rbeg1 = min_beg1;
vntr.exact_rend1 = max_end1;
if (seq_len) free(seq);
}
