/** Return the sequence of the specified contig node. The sequence
* may be ambiguous or reverse complemented.
*/
static Sequence sequence(const Contigs& contigs, const ContigNode& id)
{
if (id.ambiguous()) {
string s(id.ambiguousSequence());
if (s.length() < opt::k)
transform(s.begin(), s.end(), s.begin(), ::tolower);
return string(opt::k - 1, 'N') + s;
} else {
const Sequence& seq = contigs[id.id()].seq;
return id.sense() ? reverseComplement(seq) : seq;
}
}
/** Return the sequence of the specified contig node. The sequence
* may be ambiguous or reverse complemented.
*/
static const Sequence getSequence(ContigNode id)
{
if (id.ambiguous()) {
string s(id.ambiguousSequence());
if (s.length() < opt::k)
transform(s.begin(), s.end(), s.begin(), ::tolower);
return string(opt::k - 1, 'N') + s;
} else {
string seq(g_contigs[id.id()]);
return id.sense() ? reverseComplement(seq) : seq;
}
}
