Add "tseq" output & make available to Python

[nickzoic]

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]

G'day @lh3 just wondering if you've had a chance to consider this one? I've rebased it so it should work against current master. The purpose is to extract the sequence matched against so that it's easier to extract the differences.

[lh3]

You can use mappy.Aligner.seq() to retrieve reference subsequences.

[nickzoic]

Oh, awesome, I'd missed that!

That means I can get what I need using aligner.seq(alignment.ctg)[alignment.r_st:alignment.r_en].

Thanks!

[lh3]

Better use aligner.seq(alignment.ctg, alignment.r_st, alignment.r_en)