Reject piped input (/dev/stdin) for BedToIntervalList #1918
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
|
For #1890 |
cmnbroad
reviewed
Mar 12, 2024
| @@ -114,8 +114,13 @@ public class BedToIntervalList extends CommandLineProgram { | |||
| @Override | |||
| protected int doWork() { | |||
| IOUtil.assertFileIsReadable(INPUT); | |||
| if(INPUT.getPath().equals("/dev/stdin")) { | |||
| throw new IllegalArgumentException("BedToIntervalList cannot read from /dev/stdin."); | |||
There was a problem hiding this comment.
This is a bit of a nit, but this error message could be interpreted to mean that reading from the input is acceptable, but just failing for some reason - I would suggest explicitly stating that reading from stdin is not supported:
Suggested change
| throw new IllegalArgumentException("BedToIntervalList cannot read from /dev/stdin."); | |
| throw new IllegalArgumentException("BedToIntervalList does not support reading from standard input - a file must be provided"); |
We should also add a test to verify this.
@kockan I'm happy to make these changes if you like - just let me know.
There was a problem hiding this comment.
@cmnbroad Of course, please feel free to push to my branch
cmnbroad
force-pushed
the
can_bed2intervallist_stdin_check
branch
from
4a8976f
to
ccdbb90
Compare
droazen
approved these changes
Mar 12, 2024
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Outdated suggestions cannot be applied.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.
As the title states, reject piped input (/dev/stdin) for BedToIntervalList since it cannot process such input.