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magicDGS / thaplv

Tools for Haploid/Haplotype VCFs
BSD 3-Clause "New" or "Revised" License
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GetFasta using intervals #54

Open magicDGS opened 7 years ago

magicDGS commented 7 years ago

Maybe a better approach to allow using intervals and extract just one region will be using a IntervalWalker with require reference and variant input.

For each interval, we use the ReferenceContext for getting the bases and the list of variants from the FeatureContext to get the variants overlapping the interval and substitute for each sample the simple bases.

This should be quite straightforward, and will improve the usage of GetFasta to use with custom intervals...

magicDGS commented 7 years ago

We should generate a new engine to allow to do not pass any interval to the tool, and walk over all the genome chromosome by chromosome as it is currently done...