Added working remapping using offline code from counsyl. Required resources are located in /lovd/remapping/resources. Includes genome reference FASTA and refseq list.
Modified scripts to use new remapping functionality from Counsyl. Ported to python 2.7 compatible code to enable use of required tools.
Added function to remap from VCF to HGVS.
General code cleanup and minor refactoring - particularly of VCF file text generation.
Updated script to use modified remapping libraries. Also added two command line parameters so that you can specify what the column labels for the hgvs notation and protein change columns are. This allows it to be applied to any tab-delimited file containing this information. May want to specify flags on command line for these rather than purely using the order.
Bug fix where modified VCF file generation messed up the header line formatting (added many additional tab characters). General code cleanup and some added documentation.
Fixed bug in file writing function where unicode strings were not properly decoded before writing out. This is unique to python 2 and was not an issue due to all unicode policy in python 3 (handles this decoding automatically). Other minor cleanup and documentation updates.
Updated refseq definitions to provide more reference transcripts. Added additional scripts to convert downloads from UCSC to usable formats and merge new and old definitions if updates needed in the future.