polyTG enhancements

[rjsicko]

if we check polyTG job hook on a targeted mutation run, the script should check for this and simply output "polyTG not run, targeted mutation run"

"is_only_report_targeted_mutations": true,

[rjsicko]

also, should probably error check better in script.

failed samples, ntc etc. might be killing the script with divide by zeros etc.

[rjsicko]

if we check polyTG job hook on a targeted mutation run, the script should check for this and simply output "polyTG not run, targeted mutation run"

"is_only_report_targeted_mutations": true,

could we get the polyT script to run on 2nd tier and then only output the calls if there is a variant called? only trouble is the VHIRT...

[rjsicko]

another enhancement - 'action' column.
pseudocode
if(call in "haplotypes_of_interest_list"){ action="validate and report"}elif(call in "haplotypes_benign"){action="no action necessary"}else{action="unknown haplotype, validate, interpret and report if interpretation is VOUS, LP, P"}