fn() consensusAlignment
Compute consensus alignment.

Defined in <seqan/consensus.h>
Signature void consensusAlignment(alignmentGraph, beginEndPos[, options])


alignmentGraph Alignment graph to build.
options Optional settings for the consenus alignment, type: ConsensusOptions.
beginEndPos Interval start and end position for the read's alignment; String<Pair<TPos, TPos> >.

Detailed Description


#include <seqan/sequence.h>
#include <seqan/graph_align.h>
#include <seqan/consensus.h>
int main()
    using namespace seqan;
    typedef StringSet<Dna5String> TStringSet;
    typedef Graph<Alignment<TStringSet, void, WithoutEdgeId> > TAlignGraph;
    TStringSet readSet;
    String<Pair<TSize> > begEndPos;
    appendValue(readSet, "CCCAGTGA");
    appendValue(begEndPos, Pair<TSize>(0, 5));
    appendValue(readSet, "AGGGACTGT");
    appendValue(begEndPos, Pair<TSize>(3, 9));
    TAlignGraph alignmentGraph(readSet);
    consensusAlignment(alignmentGraph, begEndPos);
    return 0;