Add bw_long option to mappy's Aligner class #1124
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
The Minimap2 behavior was found to handle sequences with large deletions differently when upgraded from v2.17 to v2.26, causing potential issues in projects mapping extensive deletions of ~1200 base pairs. The originally suggested solution of setting `-r 500,500` was observed to be partially non-applicable since the Python Wrapper, `mappy`, only allowed manipulation of parameter `bw`. In response to issue lh3#1111, where this was originally reported, this commit introduces a modification in the Python wrapper, `mappy`. Until now, `mappy` only allowed manipulation of the `bw` parameter, preventing the suggested fix of setting `-r 500,500`. This commit introduces a modification in the Python wrapper to include the `bw_long` option in the `Aligner` class. Consequently, both parameters `bw` and `bw_long` can be manipulated, thereby allowing the desired Minimap2 behavior encountered in version 2.17. As a result, this patch ensures consistent handling of sequences containing large deletions irrespective of the version upgrade." Closes lh3#1111
|
Thanks! |
kojix2
added a commit
to kojix2/ruby-minimap2
that referenced
this pull request
Mar 13, 2024
Donaim
added a commit
to cfe-lab/MiCall
that referenced
this pull request
Oct 24, 2024
Since minimap base algorithm changed between versions, this update requires setting the bw and bw_long options to retain the original behaviour. See lh3/minimap2#1124 for more details. Also, the quality calculation was adjusted in minimap. This is not a significant change for us because that quality metrics is not actually used anywhere.
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.
The Minimap2 behavior was found to handle sequences with large deletions differently when upgraded from v2.17 to v2.26, causing potential issues in projects mapping extensive deletions of ~1200 base pairs. The originally suggested solution of setting
-r 500,500was observed to be partially non-applicable since the Python Wrapper,mappy, only allowed manipulation of parameterbw.In response to issue #1111, where this was originally reported, this commit introduces a modification in the Python wrapper,
mappy. Until now,mappyonly allowed manipulation of thebwparameter, preventing the suggested fix of setting-r 500,500.This commit introduces a modification in the Python wrapper to include the
bw_longoption in theAlignerclass. Consequently, both parametersbwandbw_longcan be manipulated, thereby allowing the desired Minimap2 behavior encountered in version 2.17. As a result, this patch ensures consistent handling of sequences containing large deletions irrespective of the version upgrade."Closes #1111