Legacy honeycomb structure shifted in lattice by v2decoder

[cmaffeo]

Problem

The helices in the legacy json file get placed in the wrong row by the cadnano2.5 v2decoder (see images below). I'm not sure about other design files.

cadnano2

cadnano2.5

Possible fix

Inserting 'delta_row += 1' after line 68 in cadnano/fileio/v2decode.py fixed the issue for this structure, but this might not be general.

[cmaffeo]

The fix suggested above is no good because it flips the assignment of fwd/rev strands, which was correct for my test cases.

As a possible alternative, I've uploaded a patch that swaps the conditional in the legacyLatticeCoordToPositionXY method in lattice.py and conditionally shift the row index for honeycomb structures in v2decoder.py.

The patch works for a couple of json files I have laying around and for the files in the cadnano/tests/data directory, but it might affect the c25decoder. Also the blue grid in the background can become shifted so it lies outside the red box in the left panel of cadnano, which probably needs to be fixed.