Allow haplotypes and alignments to have left, right, samples params

[hyanwong]

Description

Adds "samples", "start", and "stop" parameters to ts.haplotypes() and ts.alignments(). This (partially) fixes #2092. I was worried that calling var.decode(site_id) by simply iterating over the site ids would be slow, but that's how the sites() method does it anyway.

Is this the right approach? I haven't written any new tests until it's deemed sensible.

PR Checklist:

• Tests that fully cover new/changed functionality.
• Documentation including tutorial content if appropriate.
• Changelogs, if there are API changes.

[codecov]

Codecov Report

Merging #2397 (31b7e63) into main (b74b98c) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #2397   +/-   ##
=======================================
  Coverage   93.33%   93.33%           
=======================================
  Files          28       28           
  Lines       26952    26977   +25     
  Branches     1236     1245    +9     
=======================================
+ Hits        25155    25180   +25     
  Misses       1763     1763           
  Partials       34       34           

Flag	Coverage Δ
c-tests	92.25% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	71.00% <9.75%> (-0.11%)	⬇️
python-tests	98.96% <100.00%> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
python/tskit/trees.py	98.66% <100.00%> (+0.01%)	⬆️

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[benjeffery]

(Note that as written your description will close #2092)

Should variants also get start and stop? Not sure why it shouldn't. And yes using decode is the way to do this. All the heavy lifting is in seeking and decoding so the Python overhead isn't bad.

[hyanwong]

(Note that as written your description will close #2092)

Yep, That was basically deliberate. I will open a new issue with the unaddressed bits there.

Should variants also get start and stop? Not sure why it shouldn't.

I guess it could. Do you want me to add it to this PR then?

[hyanwong]

p.s. do we want "start" and "stop" or "left" and "right"?

[benjeffery]

p.s. do we want "start" and "stop" or "left" and "right"?

Everywhere else that we talk about genomic intervals we talk about left, right, so that seems to make the most sense.

[hyanwong]

p.s. do we want "start" and "stop" or "left" and "right"?

Everywhere else that we talk about genomic intervals we talk about left, right, so that seems to make the most sense.

I agree. It's clearly a genomic position if we say left and right.

[benjeffery]

@hyanwong Is this ready for review?

[hyanwong]

@hyanwong Is this ready for review?

Yes, it is.. Thanks Ben.

[benjeffery]

LGTM!
Thanks for picking this one up - great to use all the new Variant machinery.

[hyanwong]

Changes made. Would be nice to merge before the new point release, but whatever.

[jeromekelleher]

We prefer pytest.mark.parametrize for this sort of thing going forward