[hail] Implement concordance in Python.#6224
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danking merged 4 commits intohail-is:masterfrom May 31, 2019
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This is unfortunately about 2x slower -- partly due to the fact that the column + global concordance calculations are not fused, and partly because the AggArrayPerElement stuff seems pretty slow right now and is dragging down the per-sample concordance.
patrick-schultz
previously requested changes
May 31, 2019
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| def concordance2(left, right, *, _localize_global_statistics=True): | ||
| print('conc2') |
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The print is clearly debugging code. Is concordance2 itself also?
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whoops! Yes, the whole function can be removed.
patrick-schultz
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May 31, 2019
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patrick-schultz
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Just one thought, which you're free to ignore. Otherwise looks good.
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| lit = hl.literal(included, dtype=hl.tset(hl.tstr)) | ||
| left = left.filter_cols(lit.contains(left.col_key[0])) | ||
| right = right.filter_cols(lit.contains(right.col_key[0])) |
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This might be faster using semi_join_cols. I assume the semi-join is an ordered merge, so linear, while this is n log n, doing a binary search for each column.
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semi join can't do an ordered merge -- we don't store the columns ordered
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Oh of course. Never mind!
patrick-schultz
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May 31, 2019
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This is unfortunately about 2x slower -- partly due to the fact
that the column + global concordance calculations are not fused,
and partly because the AggArrayPerElement stuff seems pretty
slow right now and is dragging down the per-sample concordance.