Refactor two header determination #46
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
rhpvorderman
force-pushed
the
twoheader
branch
from
c12fe8f
to
a888f21
Compare
…cated second header
|
Hmm. This will not be able to correctly determine two headers for long reads on a non-seekable stream. (i.e. when using xopen's pipe methods). The buffer on io.BufferedReader is simply too small. I see no easy way to work around this, other than keeping the already existing code. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
FastqIter now returns a boolean on first iteration and a sequence record afterwards. This violates the principle of least surprise.
Two headers is now determined by peeking the file. I did not implement a full-fledged FASTQ parsing algorithm there as any errors in the FASTQ are likely revealed by FastqIter with an appropriate error.
Because of this change FastqReader._iter can now be properly typed and FastqIter can be safely and intuitively be used by other projects.
EDIT: I also found a small mistake in
_core.pyithat I have corrected here, but I could do that separately if you do not wish to merge this.fixes #38