add command to use existing lims2 design as target for new design
add command to only get oligo target region coordinates for the G oligos
add command to merge the data from the newly found G oligos with the U / D oligos of a existing design
add global-only design oligos
add new global-only design method
fix pod
add new complete cmd for creating short arm designs
use builder method on attribute to set default values for G oligo parameters
add methods to set default g oligo parameter values on the test object so we can still test the GapOligoCoordinates role
add short-arm design types
add original LIMS2 design id to logging
log a better error message if we can not find the design in LIMS2
short set of instructions for running designs into LIMS2 through command line
add hash linking oligo types to the oligo classes for gibson designs
when parsing bwa output look at the segment_unmapped and secondary_alignment flags.
Mark unmapped oligos
Store the location of the hits for each oligo
create a design comment record with detauls of oligos off target hits when they exist.
Make sure the pairs from Primer3 are used for gibson designs
added option for gibson designs to allow oligos with off target hits to be accepted.
Before this any oligo with off target hits was marked as not valid.
Also added a check for unmapped oligos.
Added tests for all the above changed
ignore perl critic issue
Merge branch 'master' into devel