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Prevent pVACvector from clipping Best Peptide #1174

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merged 2 commits into from
Jan 15, 2025
Merged

Prevent pVACvector from clipping Best Peptide #1174

merged 2 commits into from
Jan 15, 2025

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susannasiebert
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When running the pvacseq generate_protein_fasta command in combination with an aggregated report as the --input-tsv the output fasta will now contain information about the Best Peptide for mutant fasta entries. This information is then used by pVACvector to prevent clipping into the Best Peptide.

Closes #1164

@susannasiebert susannasiebert linked an issue Jan 7, 2025 that may be closed by this pull request
Prevent pVACvector from clipping epitopes #1164
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chrisamiller
chrisamiller approved these changes Jan 7, 2025
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This looks great. I briefly considered whether this best peptide check should be an option, instead of running all the time, but I'm struggling to come up with a scenario where we'd want to turn it off, so as is seems fine. +1

Base automatically changed from pvacvector to staging January 15, 2025 14:40
@susannasiebert susannasiebert merged commit 6f19436 into staging Jan 15, 2025
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@susannasiebert susannasiebert deleted the pvacvector_clipping branch January 17, 2025 18:48
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@chrisamiller chrisamiller chrisamiller approved these changes

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Prevent pVACvector from clipping epitopes
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@susannasiebert @chrisamiller