mappy check index flags before mapping #1008
Merged
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
mappy creates a CIGAR string by default (`-c` flag) and so is incompatible with indexes that are created using the `--idx-no-seq` flag. The previous implementation of mappy did not check for the `MM_I_NO_SEQ` flag and would seg fault when attempting to map a read or retrieve a reference sequence from the index. This patch adds a check to both `mappy.Aligner.seq` and `mappy.Aligner.map` and returns `None` if there is no index sequences. I've chose `None` as this is inline with the behaviour of mappy for reads that do not align/retreiving sequences that aren't in the index, however it might be better to raise an exception so that this error is distinct and can be communicated to the caller.
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Outdated suggestions cannot be applied.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.
mappy creates a CIGAR string by default (
-cflag) and so is incompatible with indexes that are created using the--idx-no-seqflag.The previous implementation of mappy did not check for the
MM_I_NO_SEQflag and would seg fault when attempting to map a read or retrieve a reference sequence from the index. This patch adds a check to bothmappy.Aligner.seqandmappy.Aligner.mapand returnsNoneif there is no index sequences. I've choseNoneas this is inline with the behaviour of mappy for reads that do not align/retrieving sequences that aren't in the index, however it might be better to raise an exception so that this error is distinct and can be communicated to the caller.closes #1007