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Add "tseq" output & make available to Python

Open nickzoic opened this issue 10 months ago • 0 comments

It'd be handy to be able to retrieve the sequence which minimap2 has matched with, to generate HGVS strings or etc.

You could reconstruct this from the long form CS string (see #1194) but it seems like it'd be handy to just retrieve the whole string in one go.

This PR adds an mm_gen_tseq C function to retrieve the sequence, and a tseq property on the python Alignment object.

I've called it "tseq" because it's called that in the write_cs_ds_or_MD function but it's not necessarily a great name.

nickzoic avatar Apr 25 '24 07:04 nickzoic