N-masked sequence may be ignored, no track feature created

[jduvick]

A dataset with Volvox carterei genome scaffolds, containing N-spacers (3.7 % of total according to xGDBvm's file validation script), was found to be incorrectly parsed for what we term 'N-masked' regions.

Specifically, no N-masked regions were parsed by the script parseGsegMask.pl, resulting in and empty ~mask.fa file and a WARNING flag 6.40 in the Pipeline_Procedure.log. I can reproduce the problem but haven't found the source yet. One difference from the Example 1 benchmark for N-mask parsing is that V.carterei genome segments include lower case (gatc) bases, although the N-masked sequence interspersed is uppercase.