Fix scaling: take chromsizes from header #239
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pairtools/tests/test_scaling.py Line 27 in 8c41a26 Are single unmapped pairs somehow supposed to contribute to scaling? I think this might be why the test fails... |
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nah, they are never counted.
…On Fri, 3 May 2024 at 15:34, Ilya Flyamer ***@***.***> wrote:
https://github.com/open2c/pairtools/blob/8c41a26b3f3a3905e307f3baa4b547203394dca1/tests/test_scaling.py#L27
Are single unmapped pairs somehow supposed to contribute to scaling? I
think this might be why the test fails...
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Then why does the test assert 9 total pairs? It doesn't make sense to me, but somehow I guess this test was passing before? |
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(As an aside, in the file there is a pair with both sides beyond the end of the chromosome... should that actually error or warn at least?) |
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OK, I think I know where the problem is: when not chromsizes are provided, internally they are created from the data, and then there is a fake chrom "!" which I guess just behaves like any other chromosome... pairtools/pairtools/lib/scaling.py Line 143 in 8c41a26 So I would say the test is wrong in this case? |
Phlya
commented
Jun 4, 2024
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| if isinstance(pairs, pd.DataFrame): | ||
| pairs_df = pairs | ||
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| elif isinstance(pairs, str) or hasattr(pairs, "buffer") or hasattr(pairs, "peek"): | ||
| pairs_df, _, _ = pairsio.read_pairs(pairs, nproc=nproc_in, chunksize=chunksize) | ||
| pairs_df, _, chromsizes = pairsio.read_pairs( |
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@golobor can we merge this? |
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Scaling without a view was broken! Docs said it would use the chromsizes from the header, but there was no code that was doing it...