Function
matchRefinement
Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
matchRefinement(matches,stringSet,scoringScheme,refinedGraph,minFragmentLen)
matchRefinement(matches,stringSet,refinedGraph,minFragmentLen)
matchRefinement(matches,annotation,stringSet,scoringScheme,refinedGraph)
matchRefinement(matches,annotation,stringSet,scoringScheme,refinedGraph,minFragmentLen)
matchRefinement(matches,annotation,stringSet,refinedGraph,minFragmentLen)
matchRefinement(matches,annotation,stringSet,refinedGraph)
matchRefinement(matches,stringSet,scoringScheme,refinedGraph)
matchRefinement(matches,stringSet,refinedGraph)
Parameters
minFragmentLen
The minimal segment length allowed (unsigned int).
Remarks: If in the refinement process a cut would result in a segment shorter than minFragmentLen, then the cut is not made and a heuristic is applied to refine this short overlap.
If no minFragmentLen is given, then all cuts are made. This corresponds to a minFragmentLen of 1.
annotation
Sequence annotation data.
Types: Annotation
matches
The set of matches.
The set of matches.
scoringScheme
The scoring scheme used to score the refined matches (scores are attached to edges in the refined Alignment Graph).
Types: Score
Remarks: If no scoring scheme is given, all edges get weight 1.
stringSet
The StringSet containing the sequences which the matches lie on.
Types: StringSet
refinedGraph
The resulting refined set of matches stored in a graph.
Types: Alignment Graph
SeqAn - Sequence Analysis Library - www.seqan.de