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Change Nanopore defaults#144

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mbhall88 merged 14 commits intoMykrobe-tools:masterMykrobe-tools/mykrobe:masterfrom mbhall88:ont-defaultsmbhall88/mykrobe:ont-defaultsCopy head branch name to clipboardFeb 1, 2022

+45-53

Commits

Commits on Nov 4, 2021

• add stop codon to table

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  5226409

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Commits on Nov 7, 2021

• fix typo in warning message

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  7caff7f

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• improve error handling for duplicate X vars

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• add test for creating mutation with stop codon

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Commits on Nov 16, 2021

• do not include stop codons with X amino acids

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• default kmer size set to 21

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• fix failing tests due to kmer size change

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• do not assume reference file name is same as chrom

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• add panel version to JSON output

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• add shorthand CLI opts

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Commits on Nov 30, 2021

• change --ont defaults and illumina error rate [Mykrobe-tools#133 & Mykrobe-tools#134]

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• linting and removing some dead code

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Commits on Dec 1, 2021

• revert default Illumina error rate

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Commits on Jan 17, 2022

• Merge branch 'master' into ont-defaults

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