Issue with rewind when passing input through a non-seekable stream - #10
Open
WildBunnie wants to merge 1 commit into
Open
Issue with rewind when passing input through a non-seekable stream#10WildBunnie wants to merge 1 commit into
rewind when passing input through a non-seekable stream#10WildBunnie wants to merge 1 commit into
Conversation
…om pipe instead of a file
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
The parser currently uses the
rewindfunction to go back to the start of a stream, for example in theFileTypefunction. This works correctly when passing the input through stdin using a file stream:The problem is that when we pass it through a pipe or any other non-seekable stream it is unable to go back to the start causing, in the case of
FileType, the first character to disappear:bin $ cat input | ./gto_fasta_complement seq AACGTGACTGGACTTCAGAACCTCATACTGGCGCCGAGCCGAGATAGCTTGCGAGCTAGATCGCGATATCCACCACGGCTTCCGCCAGACAGCAGCATI'm currently using GTO inside the browser through WebAssembly as part of the BioChef project, and the
stdinis also passed in an non-seekable way, which causes the problem mentioned above. This pull request aims to fix this by usingungetcto put the character back in the buffer instead of usingrewind.This fix solved this specific problem for me but I only tested it for this specific use case, so I'm guessing the other places that use rewind will also have the same problem.