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Refactor pybigtools API#44

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jackh726 merged 30 commits intomasterjackh726/bigtools:masterfrom pybigtools_refactor_rebasejackh726/bigtools:pybigtools_refactor_rebaseCopy head branch name to clipboardJun 27, 2024

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Commits on Jun 20, 2024

• Extract out a BBIFile trait for pybigtools and use it in start_end

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• Merge BigWigRead and BigBedRead into BBIRead, add sql fn

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• Overhaul pybigtools API

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• Split rest into fields of tuple

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• Add is_bigwig and is_bigbed

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• Move other values creation functions to outer scope and add simplified error conversion

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• Accept i32 not u32

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• Allow passing in an array

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• Cleanup and some fixes

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• Add info fn

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• Make is_bigwig, is_bigbed properties

  

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• Add zoom_records function

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• Add close method, fix text signature of values, implement gc and context manager methods, add api test, and fix bigtools returning intervals starting at the end base

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• Move bigWigAverageOverBed to BBIFileRead

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• Use specialized Python exceptions

  

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• test: Refactor tests

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• docs: Numpy-style docstrings for methods

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• feat: Make chrom not found raise a KeyError instead of returning None

  

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• feat: Support pathlib.Path as input to open

  

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• test: Add url and filelikes to tests

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• Add doc string to custom exceptions

  

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• fix: Make chrom and end optional for values()

  

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• Fix test

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• Use nanmean instead of mean

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Commits on Jun 23, 2024

• bigBed autosql can be null, so return Option<String>

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• Bump pybigtools dev minor version

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Commits on Jun 24, 2024

• Track coverage by base

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Commits on Jun 27, 2024

• Don't use ceil for bin_start and bin_end

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• Before summing base values, max with 0 to ignore nan

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• __exit__ should not return Self (it's truthy and prevents exceptions from being raised)

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