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Instead automatic conversion from e.g. hg19 to GRCh37 we should add liftover(new_reference) as methods for both Variant and VariantCollection. Initially this will just do the almost-identity conversions between UCSC and Ensembl references. Later it would be nice to add mappings between e.g. alt contigs and even later it would be nice to actually perform liftover between different references (GRCh37 to GRCh38).
Instead automatic conversion from e.g.
hg19
toGRCh37
we should addliftover(new_reference)
as methods for bothVariant
andVariantCollection
. Initially this will just do the almost-identity conversions between UCSC and Ensembl references. Later it would be nice to add mappings between e.g. alt contigs and even later it would be nice to actually perform liftover between different references (GRCh37 to GRCh38).Once we want liftover to actually change coordinates, we should use: http://crossmap.sourceforge.net/
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