charlesbreeze/eFORGE

New example dataset works for 450k and 27k arrays

Fix buglet: don't count excluded probes as missing

Rename bkgdstats and related variables for cleaner code

Even more code cleanup

More code cleanup

Clean up the code

Use compressed files to save space on the server

More changes for v1.2

Fix mixup between strict and marginal thresholds of significance. Als… …

…o fixes pink color on dChart

New DB schema - both code and DB are data-agnostic

Copyright and authorship

Move SQL for fetching probe_id from location to eForge.pm

Fix legacy from FORGE in process_file and fetch_rsid (now called fetc… …

…h_probe_id)

Use a refarray instead of an array for mvps

Support to deploy the webserver on any URL (like http://server.org/ef… …

…orge/)

Update webcode to use eforge_1.1.db …

Also updated the copyright notice on the web page.

changes to email and copyright (still GPL) …

contact and added UCL copyright details (still GPL)

db changes in code …

changes in database to add blueprint and consolidated roadmap data

Add --autoopen options

Keep p-value in natural scale and represent the -log10 in ePlot

Use zscore method to get the zscore

Prettify the code, remove some legacy bits

Adding B-Y FDR corrected q-values to output file

Fix 27k plpatform label

Add support for different background labels …

The code is now a little smarter about checking that the background is valid and output the set of
available ones otherwise.

Change pod2usage to die call when too few MVPs

Re-order progress statements

Clean up the code after merge

27k hash addition …

Modification of eFORGE hash selection to include 27k array as an option
for background (subset of 450k probes that are on the 27k array)

New --web flag for web-server specific options …

A new --web flag is available to run code that is specific to the web server and
that breaks the standalone version of eforge.pl

Speed up eForge::process_bits …

There is a very small gain in using substr rather than split. The major gain is in
the new "if" clause within the foreach loop. It is only true if the bit is 1 (as the
bit can only be 0 or 1) and will therefore increment the counter for that cell and
push this probe to the list of MVPs for that cell.

Add warning messages for tracking progress on the web interface

Move warning message from module to main script

Fix indentation

Option proxy is now a string.