Fixes edge case where soft-cliped portion of a read ends up at a nega… #1513
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
|
Made this initial PR, waiting on tests to pass and a larger test on a full sized bam to complete. |
|
@yfarjoun We found an annoying edge case. Assuming this passes tests, could you take a look at this? |
yfarjoun
reviewed
May 21, 2020
yfarjoun
reviewed
May 21, 2020
| @@ -819,10 +819,10 @@ private static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRe | |||
|
|
|||
| // Temporarily use the newCigar that has SOFT_CLIPs replaced with MATCH_OR_MISMATCH to get read position at reference, but ignore existence of soft-clips | |||
| rec.setCigar(newCigar); | |||
| readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos, false); | |||
| readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos + posShift, false); | |||
There was a problem hiding this comment.
add a comment that since the read effectively got shifted forward by turning the clips into matches, the query position needs also to be moved forward so that it's still querying the same base
yfarjoun
approved these changes
May 21, 2020
2 tasks
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Outdated suggestions cannot be applied.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.
…tive position
Description
Give your PR a concise yet descriptive title
Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?
Mention any issues fixed, addressed or otherwise related to this pull request, including issue numbers or hard links for issues in other repos.
You can delete these instructions once you have written your PR description.
Checklist (never delete this)
Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.
Content
Review
For more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests