A method for normalizing start/end coordinate to a given Strand and CoordinateSystem in one call?

[ielis]

@julesjacobsen - how about hanging these methods on GenomicRegion to allow normalizing start/end coordinates to a given strand and coordinate system?

default int startOnStrandAndCoordinateSystem(Strand otherStrand, CoordinateSystem otherSystem) {
    int delta = coordinateSystem().startDelta(otherSystem);
    return strand() == otherStrand
            ? start() + delta
            : Coordinates.invertPosition(coordinateSystem(), end(), contig()) + delta;
}

default int endOnStrandAndCoordinateSystem(Strand otherStrand, CoordinateSystem otherSystem) {
    int delta = coordinateSystem().endDelta(otherSystem);
    return strand() == otherStrand
            ? end() + delta
            : Coordinates.invertPosition(coordinateSystem(), start(), contig()) + delta;
}

The methods above would be used instead of constructs like:

GenomicRegion transcript = ...
GenomicRegion variant = ...

GenomicRegion variantOnStrand = variant.withStrand(transcript.strand()).withCoordinateSystem(transcript.coordinateSystem());
int start

which are necessary if you want to get your hands on the coordinates, either as int or as Position. Until now, I needed to access the coordinates to:

• calculate 0-based start and end coordinates of a GenomicRegion to query Jannovar's interval tree for overlapping/neighboring items. The items are stored in the interval array using 0-based coordinates on Strand.POSITIVE

  GenomicRegion region = ... // e.g. region corresponding to <DEL>
  GenomicRegion posZeroBased = region.toPositiveStrand().toZeroBased();
  IntervalArray<Transcript> intervalArray = intervalArrayMap.get(posZeroBased.contigId());
  IntervalArray<Transcript>.QueryResult result = intervalArray.findOverlappingWithInterval(posZeroBased.start(), posZeroBased.end());
  // ... process the result

• calculate distance to upstream/downstream exon border for a variant located in the exon (an example is too out of context to be included here)

I am thinking whether we need to add this method. On one hand it would fit these use cases, on the other hand we might use the chained .toPositiveStrand().toZeroBased() here and only use the primitive-based methods for tasks like identifying overlaps, distances between regions, etc..

[ielis]

Done