Feature request: Display softclip areas as IGV does

[dformoso]

Hi all,

I wonder whether you have looked into the work needed to display softclip areas based in CIGAR data way IGV can display it. I'm working on a tool to display lateral gene transfer, and there are instances where we could benefit from the added clarity. IGV is unfortunately not practical as the tool generates images of hundreds of potential insertion sites programmatically.

Sometimes the putative insertion site is relatively obvious... as can be seen here on the right with truncated reads that partially map to another species.

Some other times much less so...

Visual confirmation of the softclipped areas would make all the difference.