First pass at trim functions

[hyanwong]

Closes #288

No tests yet, as these will be easier once #261 is committed, so that we can easily make tree sequences with no trees to left or right.

Also the documentation will need improving (e.g. document the TableCollection methods). I will do this once the general approach has been approved by @jeromekelleher .

[hyanwong]

Once #261 is in, it would be rather easy to leave slice in as a convenience function. The documentation could simply say something like "ts.slice(start, stop): a convenient wrapper for ts.keep_interval([(start, stop)]).trim().

But I'm equally happy not to have this.

[hyanwong]

The code in remove_sites duplicates code in the proposed keep_intervals() function in #261. But I think we do need to remove sites in trim, as we don't know beforehand if the TS to trim has come from keep_intervals or not. If not, we might end up with negative positions for some sites.

I suspect the remove_sites functionality is more generally useful too. I've coded it up here as a tables function, so it should be possible (although maybe less efficient) to use it in keep_intervals, if we want to reduce code duplication.

[codecov]

Codecov Report

Merging #292 into master will decrease coverage by 0.3%.
The diff coverage is 29.16%.

@@            Coverage Diff             @@
##           master     #292      +/-   ##
==========================================
- Coverage   86.25%   85.95%   -0.31%     
==========================================
  Files          20       20              
  Lines       14086    14146      +60     
  Branches     2749     2755       +6     
==========================================
+ Hits        12150    12159       +9     
- Misses       1010     1061      +51     
  Partials      926      926

Flag	Coverage Δ
#c_tests	86.82% <29.16%> (-0.42%)	⬇️
#python_c_tests	89.64% <29.16%> (-0.67%)	⬇️
#python_tests	97.5% <29.16%> (-1.71%)	⬇️

Impacted Files	Coverage Δ
python/tskit/util.py	100% <100%> (ø)	⬆️
python/tskit/tables.py	93.9% <19.51%> (-5.91%)	⬇️
python/tskit/trees.py	96.94% <35.71%> (-1.59%)	⬇️

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[jeromekelleher]

This is quite a lot of code and will need a lot of testing. Can we push this back to after 0.2.0?

[hyanwong]

Yes - I'd much prefer to prioritise getting 0.2.0 out. I've only used the trim functionality (which was in slice()) in one bit of non-reusable code anyway, so it's probably just me requiring this at the moment.

[hyanwong]

Closing with the intent of opening a new PR, since the remove_sites functionality is now coded elsewhere