* show local rather than linked feature coordinates
*/
int[] beginRange = mf.getMappedPositions(start, start);
- start = beginRange[0];
int[] endRange = mf.getMappedPositions(end, end);
+ if (beginRange == null || endRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = beginRange[0];
end = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
}
StringBuilder desc = new StringBuilder();
desc.append(sf.getType()).append(" ").append(String.valueOf(start));