Currently, Genomes are built every time the program is run. In the future, this should be revised so that Genomes are only built once, and then written to file. Then, future runs of the pipeline will import the file handles of the genomes. Currently, VariantGenome requires Variants (from VCF or other file). This requirement should be moved so that init does not require Variant insertion (variants may be pre inserted).
Options include:
file-based logic (if all genomes are derived from one genome file that == reference file, then require variants; else do not require variants (eg variants = None)
an importing flag
this may require redoing the new method of FastaGenomeAdaptor
Currently, Genomes are built every time the program is run. In the future, this should be revised so that Genomes are only built once, and then written to file. Then, future runs of the pipeline will import the file handles of the genomes. Currently, VariantGenome requires Variants (from VCF or other file). This requirement should be moved so that init does not require Variant insertion (variants may be pre inserted).
Options include: file-based logic (if all genomes are derived from one genome file that == reference file, then require variants; else do not require variants (eg variants = None) an importing flag
this may require redoing the new method of FastaGenomeAdaptor