Count reads fully spanning tandem repeats

[jzook]

In tandem repeats, it's often important to know whether reads fully span a tandem repeat in order to know whether the ALT or REF call is actually correct. I'd expect it would be useful to have an annotation related to the count of reads that support ALT and REF and fully span any repeats at the breakpoints plus ~20 bp on either side.

[nspies]

To clarify that I understand correctly, we should:

1. find repeats that overlap any breakpoint
2. for each such repeat, count how many reads fully span that repeat plus x bp to either side

Then it should be possible to see from the report:

• which breakpoints have overlapping repeats
• of those breakpoints that are repetitive, how many reads fully span those repeats