Write records sorted
Currently, the records are output sorted within each cluster, but sometimes (e.g. due to left-aligning a TS record), we extend before the prior record. I don't know yet how to implement this but it needs to be fixed as otherwise it prevents the output file to be indexed by tabix.
For example, in our test data the output record at chr13:45377983 is followed by a record for chr13:45377938:
chr13 45377983 . G A 3.86 PASS <...> GT:<...> 0/1:<...>
chr13 45377938 . GTGCCTCCCCCCCTGCGATGGGGGTCCTAAGAGCCTGGGGCGGAAGAGGGGCTGGCTCTCAGTCCGTGCCTGGCGGGGGG G 0 . CIGARETS=71M1S[TSRQR:[-2%2C2]:[-3%2C0]:23:8M:-71];AC=2;AF=2;AN=1 GT 1/1