Code

Map GTF to memory#755

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Merged

zhuchcn merged 18 commits intomainuclahs-cds/package-moPepGen:mainfrom czhu-fix-indexuclahs-cds/package-moPepGen:czhu-fix-indexCopy head branch name to clipboardJun 29, 2023

+844-295

Commits

Commits on Jun 24, 2023

• fix (GenomicAnnotationOnDisk): class created to keep genomic annotation on disk

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  8d24b62

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• fix (GenomicAnnotationOnDisk): added index_gtf function

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  53ea8dd

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Commits on Jun 25, 2023

• fix (GenomicAnnotationOnDisk): added loader function from gtf idx

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  39b9c6b

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• fix (GenomicAnnotationOnDisk): check protein coding when generating gtf index

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  dc149ca

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Commits on Jun 27, 2023

• fix (GenerateIndex): moving to use gene and tx index

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Commits on Jun 28, 2023

• fix (moPepGen): test cases passed

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• fix (moPepGen): docstrings added

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• fix (moPepGen): update version to 1.1.0

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  79771ac

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• fix (generateIndex): trying to set compression to none

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Commits on Jun 29, 2023

• fix (generateIndex): remove code to compress the copied gtf file

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  b1ac30c

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• style (moPepGen): fix pylint, added docstrings

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• doc (CHANGELOG): changelog added

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  80de41c

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• style (test)): docstrings added

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  f1554dd

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• fix (GenomicAnnotationOnDisk): gtf file handle should be uncompressed GTF file only

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  8ea2e51

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• fix (test): asserts added to GenomicAnnotationOnDisk

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• fix (test): versions of gtf idx files dont match with the github action

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  9a92ecf

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• fix (GenomicAnnotationOnDisk): remove unused import

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  8685d08

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• fix (gtf): created GTFSourceInferrer class

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