fix(qprofiler): don't assume type of SAM attribute #354
Conversation
This file contains hidden or 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
Another Check the type of the attribute before attempting to parse it to Integer/Character/etc fix #353
Contributor
Author
|
Apologies - this is hard to review because of the whole file formatting that I did. Key lines of BamSummaryReport file are 579-588, and 629-645. |
delocalizer
approved these changes
Apr 18, 2024
Contributor
delocalizer
left a comment
delocalizer
left a comment
There was a problem hiding this comment.
Looks good, thanks for the fix!
| } | ||
| } | ||
|
|
||
| parseStringAttribute(record.getAttribute("RG"), tagRGLineLengths); |
Contributor
There was a problem hiding this comment.
I understand that this parse* naming is consistent with the usage already established in this file but would you consider using instead aggregate* or accumulate* for these two new methods.
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Outdated suggestions cannot be applied.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.
Description
Updated
qprofilerso that it will only attempt to cast/parse SAM attribute into a particular type if it is aninstanceofthat type.Fixes # 353
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Unit test has been added and code has been run against BAM file that produced the error originally (successfully)
Are WDL Updates Required?
no
Checklist: