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jamesli124 merged 41 commits intomainepifluidlab/FinaleToolkit:mainfrom developepifluidlab/FinaleToolkit:developCopy head branch name to clipboardMay 10, 2024

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Commits

Commits on Apr 30, 2024

• adjust wps add support for intervals in bedgz

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• edge_size option for adjust wps

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• add Ravi to authors

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• rename agg_wps to agg_bw and move to utils

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• add hg38_gaps to GenomeGaps classmethods

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• simplify filter_bam

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Commits on May 3, 2024

• FIx end_motifs to properly calculate Shannon Entropy with kmers of 0 frequency

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• fix interval-mds to accept tsv by default

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• increment version to 0.5.1

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• update changelog

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Commits on May 6, 2024

• Merge pull request #61 from epifluidlab/fix-ux

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• create data file in tests and add small bam and frag.gz files

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Commits on May 7, 2024

• add support for Path for input_file in frag_generator

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• add basic tests for frag_generator

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• frag_generator can take frag.gz as a filepath

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• add basic opening test for end_motif

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• remove extraneous imports to test_frag_io.py

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• end_motifs accepts Path

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• update 2bit used

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• remove warning message from mds np.log and fix type hint for interval_end_motifs

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• fix type chekcing in interval_end_motifs

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• end_motifs tests

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• fix test for interval_end_motif

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• fix mds calculation for interval end motif

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Commits on May 8, 2024

• change one of assert messages

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• functional tests of CLI entrypoint

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  b741f84

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• Merge pull request #62 from epifluidlab/main

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• Add columns to docstrings for interval end motifs

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• EndMotifFreqs.to_tsv accepts instance of Path and str

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• test to_tsv for EndMotifFreqs

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• EndMotifsFreqs.from_file accepts Path

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• Rename private var EndMotifFreqs._dict to public freq_dict

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• added test for EndMotifsFreqs.from_file

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• EndMotifsIntervals methods take Path paths

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• changes to end-motifs.py

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• add tests for EndMotifsIntervals.to_tsv

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• Added test for CLI subcommand interval-mds

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  fc8a8f5

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• update changelog

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• update readme

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• Merge pull request #63 from epifluidlab/fix-ux

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• increment version number

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