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exomiser / svart

API for use in representing and manipulating genomic variation
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Add a VcfVariantFactory class #41

Closed julesjacobsen closed 3 years ago

julesjacobsen commented 3 years ago

Might be nice to encapsulate the VCF rules such as Strand and CoordinateSystem and perform trimming / breakend parsing to return a Variant from some relatively consistent input similar to the DefaultVariant.oneBased() methods.

Variant simple = VcfVariant.of(chr, id, pos, ref, alt);

Variant symbolic = VcfVariant.of(chr, id, pos, ref, alt, end, ciPos, ciEnd, svlen);

Variant breakend = VcfVariant.of(chr, id, pos, ref, alt, ciPos, ciEnd, mateId, eventId);
julesjacobsen commented 3 years ago

Done - 8fd5d903c9262336d19c764d73cc3d83e2da5ae3