List <GeneSequence> newEntries = new ArrayList<GeneSequence>();
for (GeneSequence sequence : genInfo.getLocations()) {
if (sequence.getStart() < start) {
String errorMessage = "Gene " + genInfo.getId() + " in chromosome " + genInfo.getChromosome() + " has overlaping part at position (" + sequence.getStart() + "," + start + "). Can not continue.";
LOG.error(errorMessage);
throw new GenomeFileParsingException(errorMessage);
}
if (sequence.getStart() != start) {
LOG.warn("Gene " + genInfo.getId() + " in chromosome " + genInfo.getChromosome() + " has missing part at position (" + start + "," + (sequence.getStart() - 1) + "). Assuming non coding sequence.");
GeneSequence seq = new GeneSequence(sequence.getParentId(), false, start, sequence.getStart() - 1, sequence.getDirection());
newEntries.add(seq);