* patch to ensure gene to chromosome mapping is complete
* (in case created before gene length was known)
*/
- MapList geneMapping = loci.getMapping();
+ MapList geneMapping = loci.mapping;
if (geneMapping.getFromRanges().get(0)[1] == 0)
{
geneMapping.getFromRanges().get(0)[0] = gene.getStart();
List<int[]> transcriptRange = Arrays.asList(new int[] {
transcript.getStart(), transcript.getEnd() });
MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
- GeneLoci gl = new GeneLoci(loci.getSpecies(), loci.getReference(),
- loci.getChromosome(), mapList, loci.isForwardStrand());
+ GeneLoci gl = new GeneLoci(loci.species, loci.assembly,
+ loci.chromosome, mapList);
transcript.setGeneLoci(gl);
}