uclahs-cds / package-moPepGen

Multi-Omics Peptide Generator
https://uclahs-cds.github.io/package-moPepGen/
GNU General Public License v2.0
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Added fuzz test log reseults #815

Closed zhuchcn closed 1 year ago

zhuchcn commented 1 year ago

Description

This is the last batch fuzz test results

3 issues fixed in this PR:

  1. When creating peptide cleavage graph, when a variant bubble is processed and cleaved, we need to identify the correct downstream connecting node(s) to put them into the next iteration. While doing that, only in-frame nodes should be used. However, the downstream node may be hybride, meaning it spans over multiple reading frames. So we should compare the reading frame index of the last segment of the node rather than the first.
  2. When finding variant peptides from PCG from circRNA, we need to inspect the last nucleotide of the upstream node(s) and the first nucleotide of the downstream node(s) to take into consideration of any cleavage altering variants. However the upstream node variant with downstream_cleavage_altering and the downstream node variant with upstream_cleavage_altering should not be considered, because they are carried over manually.
  3. When creating peptide cleavage graph, if the node has exactly 1 cleavage site and it has multiple incoming node, a "merge-forward" should be used. However the downstream node was not returned correctly.

Closes #...

Checklist

zhuchcn commented 1 year ago

I restarted the fuzz test a couple of times because the previous fix was not successful and also new issues found. It's running again now with 28,865 finished. Will merge this shortly if it maintains all pass.

zhuchcn commented 1 year ago

51501/51501 passed. Merging now.

lydiayliu commented 1 year ago

Should i start CPCG? a release would be ideal!