/** 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; } }