private void addGene(
Map<String, Gene> map, String gene, String chr, long start, long end, long len) {
if (map.containsKey(gene)) {
Gene geneObj = map.get(gene);
// move start
if (geneObj.getStart() > start) {
geneObj.setStart(start);
}
// move end
if (geneObj.getEnd() < end) {
geneObj.setEnd(end);
}
// update length
geneObj.setLen(geneObj.getLen() + len);
} else {
Gene geneObj = new Gene(gene, chr, start, end, len);
map.put(gene, geneObj);
}
}