| 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
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