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Add functions to support padding and filtering intervals: filter_by_intervals, pad_intervals, parse_locus_intervals #752

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merged 11 commits into from
Jan 14, 2025
Merged

Add functions to support padding and filtering intervals: filter_by_intervals, pad_intervals, parse_locus_intervals #752

merged 11 commits into from
Jan 14, 2025

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jkgoodrich
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@jkgoodrich jkgoodrich requested a review from KoalaQin January 10, 2025 17:36
@KoalaQin KoalaQin changed the title Add functions to support padding and filtering intervals: pad_intervals, filter_by_intervals, pad_intervals, parse_locus_intervals Add functions to support padding and filtering intervals: filter_by_intervals, pad_intervals, parse_locus_intervals Jan 10, 2025
KoalaQin
KoalaQin reviewed Jan 12, 2025
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Looks good. Thanks for separating the functions. I have a few comments.

gnomad/utils/filtering.py
Comment on lines +566 to +569
.. note::

If no Gencode Table is provided, the default version of the Gencode Table
resource for the genome build of the input Table/MatrixTable will be used.
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I think the note here is a bit redundant, since it's already mentioned in filter_gencode_ht function.

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I don't think it hurts to have it here for users that don't realize this function is using that function

gnomad/utils/filtering.py

if is_expr:
_ht = intervals._indices.source
num_intervals = _ht.count()
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num_intervals is only checked when the intervals is_exper, what if a list is bigger than our max? The list won't cause a memory issue?

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I think the memory issue is in the collect right? So the user will already have encountered that

KoalaQin
KoalaQin reviewed Jan 12, 2025
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jkgoodrich
jkgoodrich commented Jan 14, 2025
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jkgoodrich
jkgoodrich commented Jan 14, 2025
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@jkgoodrich jkgoodrich requested a review from KoalaQin January 14, 2025 00:32
jkgoodrich
jkgoodrich commented Jan 14, 2025
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KoalaQin
KoalaQin approved these changes Jan 14, 2025
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LGTM!

@jkgoodrich jkgoodrich merged commit 538ecf2 into main Jan 14, 2025
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@jkgoodrich jkgoodrich deleted the jg/add_support_for_padding_and_filtering_intervals branch January 14, 2025 14:32
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@jkgoodrich @KoalaQin