Updated default joinx version to .13 because .11 doesnt work for backfilling
Merge branch 'master' into gb_master
update vendor/gatk-protected pointer
The initial loop to determine the read_ends whould be while instead of for
update som-var blessed build
Fixed missing_header_lines to be smarter.

Polymutt0.13 includes the "BA" line but incorrectly as a FORMAT. It's actually INFO.
This code will not be tricked by this.
Merge branch 'master' into gb_master
DeNovo: initial commit of read processor parser
DeNovo: separate default read processing from other processings
DeNovo: rm genome_Size from read processor
De Novo: update var names in read processor
DeNovo: implement evaluating the condition for processing to check inst data
DeNovo: rm inst data property from read processor
Add gff symlink
bug fix valid_version array had two versions in single quotes
Updated `genome` tab completion.
Updated `gmt` tab completion.
remove object creation from perl DGI Talc Importer
added support for build37 by ignoring GL contigs
add $! to error message