make min D / U oligo gap parameters optional
remove min oligo gap command line options when testing command
fix names of test files
remove optional min oligo gap parameters from conditional design run, also set mask by lower case option to no
make min oligo gap a optional attribute, only filter oligo pairs by this when its set
work out optimal oligo gap automatically, currently set to 15% of the oligo region length
sort the oligo pairs by how close they are to the optimal oligo gap value, the closer the better
update tests for PickBlockOligoPair module
Test the new ordering method works, and that min oligo gap optional attribute is applied correctly
Also added test for negative stranded design
Updated test data as well
add alternative design data file
refactor consolidate design data command so it produces a alternative design data file as well as the original design data file for the primary design
add alt design data file to Test object
redo consolidate design data tests to take into account production of alternative design data file and refactoring of code
fix attribute name
add option to persist alternate designs to LIMS2#
add tests for persist-design step, mocked lims2-api object so we do not actually persist design
create docs folder and move TODO file there
add docs folder to prune list in dist
add oligo gap info to block oligo pair file
update TODO file
log how many alt designs we have
add alt-designs option
Merge branch 'devel'