ReadsToWiggle doesn't properly select read start and read stop

[gpratt]

The code is here:

readsToWiggle.pyx read_start = read.positions[0] read_stop = read.positions[-1]

This will only work for positive strands, negative strands will get the END of the read. Fix is easy, just need to decide if it is easier to swap out to htseq instead of re-writing.

[mlovci]

does htseq have the "start/middle/end" option?

[gpratt]

I'll wrap htseq a bit, but I like it more because it keeps read info for a bit longer, and is fairly fast.

I still don't use junction counting. Did you add in anything related to that with respect to clipper?