SvPileup should ignore reads marked as duplicates

[ameynert]

The number of pileups changes when duplicate reads are removed.

Test examples went from 575 > 283 pileups and 2030 > 550 pileups.

[nh13]

I would add an option to the tool to ignore duplicates, with default false for backwards compatibility.

[tfenne]

I'm going to disagree slightly and suggest that we add:
val includeDuplicates: Boolean = False
and bump the major version number. Seems like a big footgun to leave in place unless we think there's a good reason the majority of use cases would call for also looking at the duplicates?

[nh13]

Major bump would fine by me.