Does shift in Zelda position correlate with bicoid

Based on observations 3-4 october, 2013 that Zld- embryos seem to
have anterior peaks that aren't there.
Cosmetic tweaks to CountAllReads

Including ability to pass in directory from the command line, and to
mark the output if there are a non-multiple of 4 number of lines.
Analysis scripts October 8
Allow unknown directions and commented out lines
Allow configure to pool adjacent slices

By making a two-stage process, first reading in each line of the
configuration file, then only writing out to the makefile when I know
all the reads in that label.

Note that this does not preserve the yeast identities, so it is not
suitable for de-pooling the yeast from the combined samples, but this
also shouldn't delete directories, so I can presumably switch between
them without much loss of data.
Fix how I deal with yeast

SGD labels the fasta file one way, and the GFF file a different way, and
so ReheaderYeast should (I hope) help reconcile that.

Also, the changes to allow multiple samples get pooled in analysis broke
the way I was handling the yeast in the config file. That *should* now
be fixed.
Fixes to handling yeast

The way the last commit did it, combining the samfile header with the
body got confused. Now, there's an extra filter in that step that
converts all the names properly
Allow config to take RunConfig from command line
MakeSummaryTable now respects comments, only makes summary based on RunConfig