Error when having duplicated variants and no end positions

[leexgh]

If the input file contains duplicated variants and doesn't have end positions, the GN annotation pipeline fails with error: java.lang.NullPointerException: Cannot invoke "java.lang.Integer.compareTo(java.lang.Integer)" because the return value of "org.genome_nexus.client.GenomicLocation.getEnd()" is null .

GN annotation pipeline can handle duplications with full genomic location, or missing end position with no duplication, but throws errors for duplication AND missing end position.