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Scripts to create downsampled files#662

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Commits on Jan 8, 2024

• Move carrot-based tests to the tests directory.

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Commits on Apr 2, 2024

• Scripts to create downsampled files.

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Commits on Apr 4, 2024

• Fix lint errors.

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• Add melt_metrics_intervals

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Commits on Apr 5, 2024

• Add a downsampler for BED format.

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• Downsample wham_include_list_bed_file.

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• Add default downsampling regions file.

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• Implement both downsampler and converter & implement a base type that both derives from.

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• refactor downsamplers to transformers.

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Commits on Apr 10, 2024

• Reimplement downsampling cram files to correctly fetch pairs.

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• Rework the interface so that all the methods implement transform method.

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Commits on Apr 16, 2024

• Simplify the interface by removing BaseDownsampler & BaseConverter.

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• Convert serialized regions to .intervallist instead of using the existing file given in the json.

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• Replace hardcoded config with cli args, & ensure reference dict file is localized.

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  0ca6a91

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• fix lint

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Commits on Apr 19, 2024

• Update downsampling cram files to perform a second pass on the cram to linearly search for distant pairs.

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Commits on Apr 25, 2024

• Add an option for excluding some keys.

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• Add an option to disable searching for discordant pair reads.

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• Update default downsampling regions.

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• Remove some sites from the default downsampling regions.

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  26cae8f

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• Fix lint errors.

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