// Return a new Filter using ki as the target, and filter parameters in params.
func New(ki *kmerindex.Index, params *Params) (f *Filter) {
f = &Filter{
ki: ki,
target: ki.Seq(),
k: ki.K(),
minMatch: params.MinMatch,
maxError: params.MaxError,
tubeOffset: params.TubeOffset,
}
return
}
// Create a new Merger using the provided kmerindex, query sequence, filter parameters and maximum inter-segment gap length.
// If selfCompare is true only the upper diagonal of the comparison matrix is examined.
func NewMerger(ki *kmerindex.Index, query *linear.Seq, filterParams *Params, maxIGap int, selfCompare bool) *Merger {
tubeWidth := filterParams.TubeOffset + filterParams.MaxError
binWidth := tubeWidth - 1
leftPadding := diagonalPadding + binWidth
eoTerm := &trapezoid{Trapezoid: Trapezoid{
Left: query.Len() + 1 + leftPadding,
Right: query.Len() + 1,
Bottom: -1,
Top: query.Len() + 1,
}}
return &Merger{
target: ki.Seq(),
filterParams: filterParams,
maxIGap: maxIGap,
query: query,
selfComparison: selfCompare,
bottomPadding: ki.K() + 2,
leftPadding: leftPadding,
binWidth: binWidth,
eoTerm: eoTerm,
trapOrder: eoTerm,
valueToCode: ki.Seq().Alpha.LetterIndex(),
}
}