moved load_model to allow stream processing #203
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
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Outdated suggestions cannot be applied.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.
This PR closes #199 (I hope). As described in the issue, various longbow commands were failing when reading from
stdin. This PR changesload_model()to expect an openpysam.AlignmentFilerather than a stream or filename, and moves the call inside thewithstatement where the file is being read (which is almost always what happens immediately after loading a model from a BAM file).This should be okay to do, as the model is stored in the header if at all, and so
load_modelwill only consume the first piece of the stream and none of the reads.