Code

Add sequence quality as metadata#636

Code

Merged

atc3 merged 26 commits intomastervector-engineering/covidcg:masterfrom qual-metadatavector-engineering/covidcg:qual-metadataCopy head branch name to clipboardJan 15, 2024

+1,041-220

Commits

Commits on Oct 31, 2023

• Catch more valid passage values

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  d995e5c

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• sequence quality tracking

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  2781195

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• Adjust pangolin cores, add update tasks and explicit tempdir

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  5b24cc8

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• fix typo

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  feb641a

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• fix typo - write quality in plaintext, no gzip

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  ea30762

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• Add additional PANGO columns

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• Disable SARS2 preprocessing at the sequence copying step

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  3306016

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• Calculate ambiguity percentage, add quality metadata columns

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  407bf47

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• Disable filtering out sequences without a lineage

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• Fix typos, package versions, bug in percent_ambiguous

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  b78cc9c

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• Add new metadata cols to alpha config

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• Fix edge-case where fasta file ends on an empty entry that's still named

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• Filter out empty sequences

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Commits on Nov 1, 2023

• Fix typos in additional pango columns

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  d6d5ab7

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Commits on Nov 3, 2023

• Fix edge case where sequences don't have any feature coverage

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  c401b6b

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• Dont push empty sequences to DB

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• Sequence quality for SARS2 genbank workflow

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  b3a0133

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Commits on Nov 4, 2023

• Fix bug - no more encoding of quality stats

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  e8a6c2d

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• Fix bug - no more encoding of quality stats

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  26ccc63

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• UI and server accomodation for new quality filtering

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  2ca5aff

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• Ignore flu genbank data

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  1305714

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• Bump version to v2.7.6-qual-rc1

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Commits on Nov 5, 2023

• Merge branch 'qual-metadata' of github.com:vector-engineering/covidcg into qual-metadata

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Commits on Nov 6, 2023

• Set default GISAID lineage to unassigned -- avoid triggering non-null constraints on the DB

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  38b2f4a

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• Fix missing fields in alpha config

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  a0b6947

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• Fill in missing clade values

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