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Add new pVACsplice tool #911

Merged
merged 226 commits into from
Dec 13, 2024
Merged

Add new pVACsplice tool #911

merged 226 commits into from
Dec 13, 2024

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mrichters
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mrichters and others added 30 commits January 23, 2022 18:02
Reformat for indels when combining in pvacsplice
@susannasiebert susannasiebert force-pushed the staging branch 4 times, most recently from eaaa821 to 94434f1 Compare May 23, 2024 16:22
@mhoang22
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for the documentation for pvacsplice output file (output_file.rst) , in 'all_epitopes.tsv and filtered.tsv Report Columns' section, I think we may want to change the column named 'Protein Positions' to 'Protein Position'.
I proposed this change because:

  • this column in the all_epitopes.tsv is 'Protein Position' (without an 's') -> we should delete the 's' to keep it consistent with the actual output
  • this column notes the position of the first amino acid of the selected epitopes. Not the protein positions that the mutant affects. -> we should delete the 's' to reflect that this position is for only 1 aa

@susannasiebert
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for the documentation for pvacsplice output file (output_file.rst) , in 'all_epitopes.tsv and filtered.tsv Report Columns' section, I think we may want to change the column named 'Protein Positions' to 'Protein Position'. I proposed this change because:

  • this column in the all_epitopes.tsv is 'Protein Position' (without an 's') -> we should delete the 's' to keep it consistent with the actual output
  • this column notes the position of the first amino acid of the selected epitopes. Not the protein positions that the mutant affects. -> we should delete the 's' to reflect that this position is for only 1 aa

@mhoang22 this was actually just a typo. The column is, in fact, already called Protein Position so we just need to update the documentation to fix the incorrect column name.

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+1

@susannasiebert susannasiebert merged commit 77e92a1 into griffithlab:staging Dec 13, 2024
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