Conversation
![chatgpt-codex-connector[bot]](https://avatars.githubusercontent.com/in/1144995?s=60&v=4){kind=small}
There was a problem hiding this comment.
💡 Codex Review
Here are some automated review suggestions for this pull request.
Reviewed commit: 69ae3c08f3
ℹ️ About Codex in GitHub
Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you
- Open a pull request for review
- Mark a draft as ready
- Comment "@codex review".
If Codex has suggestions, it will comment; otherwise it will react with 👍.
Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".
| elif base.endswith(('.fa', '.fasta', '.fna')): | ||
| lines_per_read = 2 | ||
| else: | ||
| raise Exception(f"Cannot determine format (FASTA or FASTQ) for chunking from file extension: {path}") |
There was a problem hiding this comment.
This change now hard-fails chunking when the input filename does not end in one of the recognized FASTA/FASTQ extensions, even though previously --read-chunk-size worked for unwrapped FASTA regardless of filename. In environments that stream reads via temporary files/FIFOs without canonical suffixes (a common pattern in pipelines), chunking will now raise this exception and abort; please avoid making extension a hard requirement (e.g., infer from content or preserve the previous FASTA fallback).
Useful? React with 👍 / 👎.
1 participant
No description provided.