Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector #1871
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
…f no reads pass Illumina filters.
kachulis
requested changes
Apr 14, 2023
src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
Outdated
Show resolved
Hide resolved
…king if TOTAL_READS > 0 redundant, so that's removed now.
Closed
1 task
Closed
1 task
Closed
1 task
rickymagner
requested changes
Apr 28, 2023
rickymagner
approved these changes
May 9, 2023
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Outdated suggestions cannot be applied.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
Create a (mostly) empty metrics file instead of giving a stacktrace if no reads pass Illumina filters.
Related to the following issue: #1862
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