Added POD info to CompareColumns.pl
Added NonRef.pl to exclude sequences that match a list of names
Added AddMapMan.pl script to add MapMan annotations to a list of GeneIDs
Added GetSeqsByGeneID.pl script to extract sequences that correspond to a list of GeneIDs.
Modified FlattenBlast function in FileParser.pm to reverse coordinates of reverse-strand result

Negative strand blast results have an End coordinate with a smaller value than the start
coordinate. These coordinates get reversed during parsing, but I had neglected to reset
them when I flattened the result for printing.
Modified ScafTranscripts.pl to add info about skipped contigs to log and to avoid unnecessary seq lookups

Contigs that have 45 bp or more of non homologous overlap with their top hit (ie; alignment
starts/ends >45 bp from start/end of both query and hit) are not scaffolded but are simply
written to the outfile. Previously, this was not noted in the log. They were indistinguishable
from singleton contigs. I modified the log to indicate that these contigs have too much
non-homologous sequence.

I also moved the lookup of the contig sequence to right before it is written to file
because many contigs were being retrieved but not written. This was necessary Previously
because I had to look up the length of the sequence to determine the overlap. This information
is now provided in the blast result, so the lookups were unnecessary at that stage.
Added TopHit.pl which excludes all but the top hit for each query and all but the top query for each hit
Updated README to include info about scripts added in the last 2 days
Updated POD info for several scripts