bool gth_backtrace_path_is_valid(const GthBacktracePath *bp)
{
bool is_valid;
gt_assert(bp);
gt_assert(bp->alphatype == DNA_ALPHA || bp->alphatype == PROTEIN_ALPHA);
gt_assert(bp->ref_dp_length != GT_UNDEF_ULONG);
is_valid =
gt_eops_equal_referencelength((Editoperation*)
gt_array_get_space(bp->editoperations)
+ bp->cutoffs.end.eopcutoff,
gt_safe_cast2long(gt_array_size(bp
->editoperations))
- bp->cutoffs.start.eopcutoff
- bp->cutoffs.end.eopcutoff,
gt_safe_cast2long(bp->ref_dp_length)
- bp->cutoffs.start.referencecutoff
- bp->cutoffs.end.referencecutoff,
bp->alphatype == PROTEIN_ALPHA);
return is_valid;
}
/* XXX: change this function: add more sophisticated extension strategy */
void gth_chain_extend_borders(GthChain *chain, const GtRange *gen_seq_bounds,
const GtRange *gen_seq_bounds_rc,
GT_UNUSED unsigned long gen_total_length,
GT_UNUSED unsigned long gen_offset)
{
long tmpborder;
/* at least one range in chain */
gt_assert(gt_array_size(chain->forwardranges));
/* forward range borders are in considered genomic region */
gt_assert(gt_ranges_borders_are_in_region(chain->forwardranges,
gen_seq_bounds));
/* reverse range borders are in considered genomic region */
gt_assert(gt_ranges_borders_are_in_region(chain->reverseranges,
gen_seq_bounds_rc));
/* chain->forwardranges is forward and consecutive */
gt_assert(gt_ranges_are_consecutive(chain->forwardranges));
/* valid sequence bounds */
gt_assert(gen_seq_bounds->start <= gen_seq_bounds->end);
gt_assert(gen_seq_bounds_rc->start <= gen_seq_bounds_rc->end);
/* set start border, forward strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_first(chain->forwardranges))
->start);
tmpborder -= DPEXTENSION;
if (tmpborder < gt_safe_cast2long(gen_seq_bounds->start))
tmpborder = gen_seq_bounds->start;
((GtRange*) gt_array_get_first(chain->forwardranges))->start =
gt_safe_cast2ulong(tmpborder);
/* set start border, reverse complement strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_first(chain->reverseranges))
->start);
tmpborder -= DPEXTENSION;
if (tmpborder < gt_safe_cast2long(gen_seq_bounds_rc->start))
tmpborder = gen_seq_bounds_rc->start;
((GtRange*) gt_array_get_first(chain->reverseranges))->start =
gt_safe_cast2ulong(tmpborder);
/* set end border, forward strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_last(chain->forwardranges))
->end);
tmpborder += DPEXTENSION;
if (tmpborder > gt_safe_cast2long(gen_seq_bounds->end))
tmpborder = gen_seq_bounds->end;
((GtRange*) gt_array_get_last(chain->forwardranges))->end =
gt_safe_cast2ulong(tmpborder);
/* set end border, reverse complement strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_last(chain->reverseranges))
->end);
tmpborder += DPEXTENSION;
if (tmpborder > gt_safe_cast2long(gen_seq_bounds_rc->end))
tmpborder = gen_seq_bounds_rc->end;
((GtRange*) gt_array_get_last(chain->reverseranges))->end =
gt_safe_cast2ulong(tmpborder);
gt_assert(chain_is_filled_and_consistent(chain, gen_total_length,
gen_offset));
}
void gth_sa_calc_polyAtailpos(GthSA *sa, const unsigned char *ref_seq_tran,
GtAlphabet *ref_alphabet)
{
GtUword ppa, mma, rightreferenceborder, referencelength;
GtWord i, leftreferenceborder;
sa->polyAtailpos.start = 0;
sa->polyAtailpos.end = 0;
ppa = mma = 0;
rightreferenceborder = ((Exoninfo*) gt_array_get_last(sa->exons))
->rightreferenceexonborder;
leftreferenceborder = ((Exoninfo*) gt_array_get_first(sa->exons))
->leftreferenceexonborder;
/* setting i */
referencelength = gth_sa_ref_total_length(sa);
if ((rightreferenceborder + 1) >=
(referencelength - 1 - CALCPOLYATAILWINDOW)) {
i = gt_safe_cast2long(rightreferenceborder + 1);
}
else {
if (referencelength < 1 + CALCPOLYATAILWINDOW)
i = 0;
else
i = referencelength - 1 - CALCPOLYATAILWINDOW;
}
for (/* i already set */; i < gt_safe_cast2long(referencelength); i++) {
if (ref_seq_tran[i] == gt_alphabet_encode(ref_alphabet, 'A'))
ppa++;
else {
if (ppa > 0 && mma < 1) {
mma++;
continue;
}
else {
if (ppa >= MINIMUMPOLYATAILLENGTH)
break;
else {
ppa = mma = 0;
continue;
}
}
}
}
if (ppa >= MINIMUMPOLYATAILLENGTH) {
sa->polyAtailpos.start = gt_safe_cast2ulong(i - ppa - mma);
sa->polyAtailpos.end = i - 1;
}
else {
ppa = mma = 0;
/* setting i */
if ((leftreferenceborder - 1) <= CALCPOLYATAILWINDOW)
i = leftreferenceborder - 1;
else
i = CALCPOLYATAILWINDOW - 1;
for (/* i already set */; i >= 0; i--) {
if (ref_seq_tran[i] == gt_alphabet_encode(ref_alphabet, 'T'))
ppa++;
else {
if (ppa > 0 && mma < 1) {
mma++;
continue;
}
else {
if (ppa >= MINIMUMPOLYATAILLENGTH)
break;
else {
ppa = mma = 0;
continue;
}
}
}
}
if (ppa >= MINIMUMPOLYATAILLENGTH) {
sa->polyAtailpos.start = gt_safe_cast2ulong(i + ppa + mma);
sa->polyAtailpos.end = i + 1;
}
}
}
