[go: up one dir, main page]
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

Fix for 2 bugs in the fastq reader: #497

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fix for 2 bugs in the fastq reader: #497

wants to merge 1 commit into from

Conversation

wdu
Copy link
Contributor
@wdu wdu commented Jun 15, 2023
  • \r\n handling may cause reading a byte past end of buffer, parser fails
  • checking end-of-file condition can only be reliably done after a call to getLine() returns NULL. One particular case is that some gzip files contain empty gzip blocks at the end of the file, which can´t be predicted by the current eof() code Tested with files provided in issue ERROR: Read name line should start with '@' #491.

This reverts commit 0ee1b3b, "fix a regression bug of FASTQ reader"

@wdu
Fix for 2 bugs in the fastq reader:
d940c2e 
- \r\n handling may cause reading a byte past end of buffer, parser fails
- checking end-of-file condition can only be reliably done
  after a call to getLine() returns NULL. One particular case
  is that some gzip files contain empty gzip blocks at the end
  of the file, which can´t be predicted by the current eof() code
  Tested with files provided in issue OpenGene#491.

This reverts commit 0ee1b3b, "fix a regression bug of FASTQ reader"
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@wdu