Substitute a new quality trimming script.

replace code that eliminated alignments mapped to multiple genes.

Use bowtie options to eliminate multiple alignments instead of post-hoc
filtering.
Don't fail if the there are multiple entries for a gene name in the knowngenes table (e.g. Shank2)
Instead choose the longest transcript from among those options and proceed as usual.  This is not the best option in
All circumstances but it is sufficient to get Shank2 working.

also the ability to choose the anchor point of the alignment seems to have gone away.
Add that back in.
Merge branch 'master' of ssh://github.com/cswarth/Morris-Lab

Conflicts:
	scripts/shiny/profiling/server.R
	scripts/shiny/profiling/ui.R
	scripts/shiny/shared/R/morrislib.R
	scripts/shiny/shared/R/profiling.R