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fq trimming#37

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brentp wants to merge 28 commits intomainfulcrumgenomics/fqtk:mainfrom trimmerfulcrumgenomics/fqtk:trimmerCopy head branch name to clipboard

+1,244-107

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Commits on Aug 16, 2023

• WIP: fq stuff

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• change max_diffs to max_overlap_error_rate

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• renaming

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Commits on Aug 17, 2023

• start of CLI stuff.

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• we have readers and writers

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• reading and writing fastqs

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• actually correct based on overlap

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Commits on Aug 18, 2023

• moving average and base-quality

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• match input output names to Tim's example

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• parsing of operations enum

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• main execution loop

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Commits on Aug 21, 2023

• copy Tim's oscillation detection from python to rust

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• more efficient identify_trim_point for oscillations

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• prevent some underflows

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Commits on Aug 22, 2023

• stub out stats

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Commits on Aug 23, 2023

• cleanup stats

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• try to clarify option usage.

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• more stats

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• bug fixes and read length stats

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• naming and length hist update

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Commits on Aug 24, 2023

• add Cargo.lock

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• logging in pair overlap

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Commits on Aug 29, 2023

• warn that output files are always bgzipped

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Commits on Oct 20, 2023

• fix erroneous warning about .gz extension

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Commits on Oct 23, 2023

• clippy: PathBuf -> Path

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• fix case where there is no overhang from R1

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• handle no overhang in r1 with adapter in r2

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Commits on Oct 24, 2023

• Io::is_gzip_path

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