SvPileup should allow some minimal filtering

[tfenne]

I'm envisioning we could add parameters like:

--min-split-reads (default: 0)
--min-read-pairs (default: 0)
--min-total-support (default: 1)

The only problem with doing this is that we would no longer be able to write the evidence BAM on the fly - we'd have to write a temporary BAM with all reads supporting all break-points, and then re-process that to remove reads/templates for breakpoints with insufficient support. That's not a big overhead - these BAMs are usually pretty small. And it would also give us a logical place to add re-sorting the BAM file into coordinate order for use in IGV.

[tfenne]

Alternatively this could be a separate tool FilterPileup that takes in the raw pileup, filters the text file and then filters the BAM file emitted by SvPileup.