Add check for duplicate records to MainVcfQc

[epiercehoffman]

We've run into a few different bugs resulting in redundant records. While we have fixed or are in the process of fixing those, it would be good to routinely check for this as part of our QC. We should add a check for duplicate records to MainVcfQc.wdl.

This check should:

• Count redundant records that exactly match on the following fields: CHROM, POS, END, SVTYPE, SVLEN, CHR2, END2, STRANDS, CPX_TYPE, CPX_INTERVALS
• Count redundant INS records that exactly match on CHROM and POS and have (a) 100%, (b) 50%, and (c) 0% size similarity based on SVLEN.
• Count redundant INS records that exactly match on CHROM and POS and have (a) identical ALT, (b) records with <INS> matching records with <INS:*>, and (c) records with <INS:*> matching records with a different subtype of <INS:*>
• Output counts as well as lists of variant IDs for the duplicate records of different categories