Make tqdm(ts.variants()) work better

[jeromekelleher]

It would be nice if this would pull out the overall length of the iter. Should be easy enough?

[jeromekelleher]

Should be straightforward, we just have to abstract the code for the variants function into an iterator class (which returns the right len), a bit like the current TreeIterator class.

[hyanwong]

Just revisiting this. The variants() method has left and right parameters, so it's a bit more complicated. An iterator would need to know not just ts.num_sites, but the number of sites between left and right. I suspect we would also want to change the trees() iterator to have left and right too (see #24), so perhaps we should implement that first, change the TreeIterator to account for that, then use the same basic function to add len to the variants iterator.

[jeromekelleher]

I don't think the trees iterator is needed for this, as we use the Tree class directly.

[hyanwong]

Sorry, I mean that the code that produces the TreeIterator wrapper could generalised to provide a wrapper that would work (subclassed, presumably) for the Variants. But only if there was a generalised way to deal with left and right.

[benjeffery]

Breakpoints are stored on the tree sequence object, and are accessible from Python, so I think that could be used to get a count of the trees in the interval for len

[hyanwong]

Breakpoints are stored on the tree sequence object, and are accessible from Python, so I think that could be used to get a count of the trees in the interval for len

Yeah, this does it, I think:

ts._check_genomic_range(left, right)
breaks = ts.breakpoints(as_array=True)
left_index = breaks.searchsorted(left, side="right")
right_index = breaks.searchsorted(right, side="left")
num_trees = right_index - left_index + 1