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Commits on Mar 4, 2025

• Upgrade to version 5.2.0

  susannasiebert

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• Merge pull request #81 from griffithlab/preferred_transcript

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• Merge pull request #79 from griffithlab/exp_speed

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• Rename option

  susannasiebert

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• Use PICK'ed value as a fallback when none of the preferred transcripts match

  susannasiebert

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Commits on Mar 3, 2025

• Allow vep annotation reporter to provide a list of preferred transcripts

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Commits on Sep 3, 2024

• Refactor vcf-expression-annotator to be faster

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Commits on Jul 1, 2024

• Fix docs typos

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Commits on Feb 5, 2024

• Upgrade to version 5.1.1

  susannasiebert

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• Merge pull request #75 from griffithlab/ref_mismatch_protein_coding

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• Update ref transcript mismatch reporter to handle protein coding variants

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Commits on Oct 17, 2023

• Update rtd build config

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Commits on Oct 16, 2023

• Update to version 5.1.0

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• Merge pull request #72 from griffithlab/issue_35

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• Merge pull request #71 from griffithlab/issue_57

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• Merge remote-tracking branch 'origin/master' into issue_57

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• Merge pull request #70 from griffithlab/issue_36

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• Merge pull request #69 from griffithlab/issue_58

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• Merge pull request #68 from griffithlab/issue_63

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• Merge pull request #67 from griffithlab/docs

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• Merge pull request #66 from griffithlab/gene_expr_id

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• Add per-strand allele counts when running vcf-readcount-annotator

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Commits on Oct 13, 2023

• Downgrade duplicate variant error to a warning and skip duplicates.

  susannasiebert

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• Output warning when VCF is annotated with the PICK flag but not transcript was PICK'ed

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Commits on Oct 12, 2023

• Fix grammar.

  susannasiebert

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• Handle case in the ref-transcript-mismatch-reporter where there is no protein position annotation

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• Prevent ZeroDivisionError errors in log output

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• Update vcf-expression-annotator documentation to clarify custom id-column parameter

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• Update the expression annotator to use the gene (ID) column in Kallisto files

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• Merge pull request #64 from griffithlab/updated_tests

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• Merge pull request #54 from griffithlab/typofix

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Commits on Oct 10, 2023

• Update docs

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Commits on Oct 5, 2023

• Update tests to run in newer Python versions

  susannasiebert

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Commits on Jan 24, 2022

• Update installation instructions to reflect that any Python 3 version >=3.5 is supported

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Commits on Nov 1, 2021

• fixing typo

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