Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Need: tool/API to autodetect fasta/fastq file type #68

Closed
mr-c opened this issue Jun 27, 2013 · 3 comments
Closed

Need: tool/API to autodetect fasta/fastq file type #68

mr-c opened this issue Jun 27, 2013 · 3 comments
Labels
enhancement Python theme:customer-oriented
Milestone
1.3

Comments

@mr-c
Copy link
Contributor

mr-c commented Jun 27, 2013

Interleaved? W/ orphans?

Must support all know Illumina/Casava versions.

Built on top of screed?

Bonus: add as much of the above as possible to the unix 'file' command magic db
@mr-c mr-c mentioned this issue Jul 10, 2013
Closed
@RamRS RamRS mentioned this issue Oct 15, 2013
Closed
@mr-c mr-c modified the milestones: 1.1+ Release, 1.0 release Apr 2, 2014
@mr-c
Copy link
Contributor Author

mr-c commented Apr 6, 2014

As per #249 (comment) we only support the most common varient of FASTQ (four line stanzas) and not the theorectically possible but rarely seen line-wrapped varient.

This makes the sniffer a lot easier if he 1st pass goal is just to distinguish between FASTA and FASTQ.

@mr-c mr-c mentioned this issue Oct 29, 2014
Merged
@mr-c
Copy link
Contributor Author

mr-c commented Dec 15, 2014

I don't think we care anymore.

@mr-c mr-c closed this as completed Dec 15, 2014
@ctb
Copy link
Member

ctb commented Dec 16, 2014

Huh, OK. I still think it'd be useful, but it's probably not relevant for khmer any more.

@mr-c mr-c modified the milestones: 1.3+, 1.3 Dec 19, 2014
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement Python theme:customer-oriented
Projects
None yet
Milestone
1.3
Development

No branches or pull requests
2 participants
@ctb @mr-c