Initial commit to not loose initial changes.
Made changes to read in web dumps from SNVs or INDELs. And also read
the custom mysql dump from Shankar.
Print header for hgmd custom annotation output.

Print unique chrom:pos:ref:alt to custom annotation file. I only take
the first entry (not the greatest -- should clean this up).

Print just the chromosome identity, not the leading chr.
Adding documentation
More mods to handle file naming on the input.
Renamed file.
Made the gene summary output an option. By default, the program now just outputs the custom annotation file. Use the --vcf and/or --gene-summary to get those files as well.
Modified git ignore to exclude gzipped perl scripts.
Code cleanup getting ready for distribution.
  * Verified output
  * Better handling multiple chrom,start,ref,alt entries
  * More documentation
  * No lines more than 80 characters long
  * Minor code logic improvements
More run time status updates.

Runs on any *.txt file in the current working directory, if there are
no files supplied on the command line.

Removed POD::Usage because it's not compatible with pp on windows.
More run time documentation

Added a README file describing how to make the perl executable
Don't track the resulting custom annotation output file.

Adding HGMD Prodessional downloaded files from 2013.3 (Sept 27, 2013 release).
But we do want to track the known correct custom annotation file in
the dat subdir, along with the original data. So we can test future
improvements to the script.

Don't know how to specify gitignore a file in the base directory only,
so instead we are unignoring the file in the dat subdir.

Also ignoring mac specific filesystem files.
Added executable compiled per the instructions in the README file.
Storing windows executable as a compressed zip file for distribution,
rather than the exe.
Storing downloaded HGMD Professional files that this script requires
as a compressed zip file. And attempting to get git to ignore the
uncompressed versions we are keeping for testing purposes. [I think I
got this to work, rebasing and joining two commits]

Keeping these files compressed now. No longer need to track.
Adding a user guide.
Changed the URL from which to download the program to Illumina's
box.com location.
Minor documentation mods based on feedback from Jennifer Becq. Program
has also been successfully tested by Mark Ross, Mike Eberle, and David
McBride.

* Fixed typo in STDERR status output of the perl script.  Added
* documentation that highlights the need to unhide custom annotation
  columns 2-4.
* Other minor documentation updates.
Updated the windows executable with the modified perl code.