Capture more mis-oriented paired end reads in breakpoint split view

[cmdcolin]

Currently paired end reads are only rendered in the breakpoint split view if they are identified as NOT "read mapped in proper pair" (sam flag 0x02)

this appears to miss some "genuinely badly paired reads" like mis-oriented reads. It often captures larger inversions because the "read mapped in proper pair" seems to strongly be related to insert size distance, but it is not turned on just because reads are mis-oriented.

Our volvox sample data has some examples of this

Current main

Show connection between all reads (e.g. the !read_mapped_in_proper_pair filter turned off)

drawing just the pair orientation on the reads themselves

arc renderer

[cmdcolin]

(there is also some brainstorm of whether these big loops capture the visual effect properly, and need for legends..ideas welcome)