lots of updates to make this work with an incremental approach to building the read depths
Numerous cleanups.
Added verbose and samtool options.   Cleaned up code that searches for gtf file.
Catch up on various changes that have accumulated in qarp code,
Modify morrislab.R to issue a warning if no matching alignments are
found, not stop!

Modify profiling/server.R to include the dataset name along with the
description when presenting a list to the user.

When looking up alignments in the database from server.R, if no
alignments are found under the Refseq name, try using the the name as
specified by the user.  This will allow a mixture of alignment to be
found, some of which are under the common name and some of which are
undet the RefSeq name.
Code to make a union gene model

This code combines exons from genes that have the same common name.
This is flawed for a number of reasons.  It seems to be overly
conservative in some ways, and not conservative enough in others.
Although it avoids combining "isoforms" that are located on different
strands or chromosomes, it will combine widely separated genes if they
have the same name, Also, depending on the curation source it may not
combine genes that really should be combined, because they don't have
an identical common name.

A "better" approach might be to combine overlapping regions?  That has
its own problems.
Long overdue comit of qarp and mds directories.

This does not attempt to tease apart to package contents from the mds
or qarp directories.  this still needs more work.
Moved almost all gitignore code to the global ignore file ~/.gitignore_global
Merge branch 'master' of https://github.com/cswarth/Morris-Lab

Conflicts:
	scripts/R/mds/R/mds.R
	scripts/shiny/profiling/server.R