Increase retry count for all GAP jobs.

Genemark-specific changes were ineffective in MGAP in practice because
the pipeline creates a "Composite" job source that ignores the other
source-specific implementations.
Added ability to plot silent mutations on a lolliplot/mutation diagram
updated ur submodule to f00981b
Don't call functions in BEGIN block
fix for indels in bam-readcount
assuming this is supposed to be $bx

It does looks like part of the reason to make the BoolExpr was just to
do error checking but it also seems like we aught to just be suing the
BoolExpr for the create call.
additional error states
change data_type to get "free" validation

A user accidentally set original_est_fragment_size to 'reverse_forward'.
Since there was no validation this was accepted.  With the data_type now
a Integer it does validation.
Bless test builds for .vcf.detailed in DV2