Comma in Quality String Bug Fix

Emergency fix for issue #158.

Faster upload

Speed up the upload to QAI for issue #152. See the 6.4 milestone for a list of all the other bugs and changes.

Blanks in sam_g2p, and uploading old project names

Close #146 sam_g2p blanks, and #147 old project names. See the 6.4 milestone for a list of all the other bugs and changes.

New HIV project

Close #145 by removing old projects and adding a new HIV project. See the 6.4 milestone for a list of all the other bugs and changes.

G2P bug fixes

Fix issues #143 and #144 in G2P by clipping to V3LOOP region from larger seed. See the 6.4 milestone for a list of all the other bugs and changes.

Add missing helper script

A new helper script wasn't being passed to some steps. See the 6.4 milestone for a list of all the other bugs and changes.

New project definitions and gap bug

We can now define new projects using the QAI screens and store them in a JSON file. Also fixed several bugs, including the gap created by majority deletions. See the 6.4 milestone for a list of all the bugs.

Occasional exceptions

The main reason for this release was a couple of exceptions that we didn't catch during our testing, plus mysteriously blank coverage plots.

• #107 exception in sam_g2p
• #109 division by zero in remap
• #105 blank coverage plots
• All the 6.3.x releases fixed many other issues.

Parallel sam_g2p

• Forgot to move sam_g2p back to the parallel processing section after #78 got fixed.
• All the 6.3.x releases fixed many other issues.

Slow Ruby

• #104 very slow sam_g2p on large samples
• #102 crash when alignment fails
• #99 ties in plurality consensus
• Closed many other issues (includes issues for all 6.3.x releases).