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Develop#80

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jamesli124 merged 90 commits intomainepifluidlab/FinaleToolkit:mainfrom developepifluidlab/FinaleToolkit:developCopy head branch name to clipboardMay 28, 2024

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Commits on Apr 30, 2024

• Merge pull request #60 from epifluidlab/develop

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Commits on May 10, 2024

• Merge pull request #65 from epifluidlab/develop

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• change cleavage profile intersect_policy to any

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• fix typo in docstring

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Commits on May 13, 2024

• Merge pull request #68 from epifluidlab/main

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• mask for zeros when calculating proportions to avoid errors

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• remove _get_contigs and add _parse_chrom_sizes

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• fix coverage verbose log

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• add numerous util functions related to merging overlapping bins

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• Changed _cli_cleavage_profile

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Commits on May 14, 2024

• Merge pull request #72 from epifluidlab/main

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Commits on May 15, 2024

• update cleavage_profile docstring

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• added chrom_sizes_to_dict

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• left and right option added to cleavage_profile

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• update cleavage-profile cli to have laft and right coordinate

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• files for cleavage_profile tests

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• fix cleavage profile with left and right options

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• add basic test for cleavage profile

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• remove unnecessary comments

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• update changelog

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• Merge pull request #73 from epifluidlab/fix-cleavage-profile

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• remove vague TODOs

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• update type hints for coverage

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• update docstring for single_coverage

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• add intersect_policy option to coverage

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• add cli option to frag-coverage and remove TODO comment

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• update typing annotations and docstring for coverage

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• replace genome2_list with chrom_sizes_to_list

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• frag_generator raises exception if contig not specified but start or stop is

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• temp files

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Commits on May 16, 2024

• Update documentation and argparse help.

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• Update documentation and argparse help.

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• Fixed some doc issues.

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• Updated CLI docs.

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Commits on May 17, 2024

• Remove comment

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• remove banana.txt

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• create separate test module for cli entry points

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• ignore test tempfiles

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• remove subcommad line that would cause tesets to fail

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Commits on May 18, 2024

• Merge branch 'develop' into temp

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• Merge pull request #76 from epifluidlab/temp

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• Merge branch 'fix-remove-todos' into develop

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• Merge pull request #77 from epifluidlab/develop

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• remove unused and redundant function

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• remove data and figs directories

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• remove conda env files

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• update readme

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• remove unnecessary dependencies

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• remove pybedtools import

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• change required Python version to 3.9

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• change Tuple type hints to tuple literal

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Commits on May 22, 2024

• change Tuple to tuple

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• fix comment

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Commits on May 23, 2024

• update changelog

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• Merge pull request #78 from epifluidlab/fix-remove-todos

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• changed filter_bam filter to match FinaleDB

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• fix docstring

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• added tests for frag_array

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• updte .gitignore

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Commits on May 24, 2024

• fix docstring

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Commits on May 26, 2024

• change order of assert statements

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• update docstring

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• change order of assert

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• create lwps test

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• update gitignore

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• update changelog

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• remove unecessary importlib_resources imports

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• remove mentions of FinaleTools

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• fix typos

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• remove unused imports

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• give cli subparsers human-readable names

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• update changelog

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• Merge pull request #79 from epifluidlab/unit-tests

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• fix type annotations

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• change version number and update changelog

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Commits on May 27, 2024

• update pyproject.toml

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• include docstring and __version__

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• include --version option

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• add -v option

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• change pyproject to dynamically generate version

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• fixed bad import in pyproject

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• update changelog

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• remove unused dependency for docs

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• update docstrings

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• index page for _documentation

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• add sphinx.ext.napoleon to parse numpy style docstrings

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• update list of methods

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• move _documentation to documentation

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