Add piped input tests for RevertSam, MergeBamAlignment #1974
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
lbergelson
approved these changes
Aug 6, 2024
| @@ -269,7 +269,7 @@ protected int doWork() { | |||
| } | |||
|
|
|||
| final boolean sanitizing = SANITIZE; | |||
| final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath()).validationStringency(VALIDATION_STRINGENCY).open(SamInputResource.of(INPUT.toPath())); // tsato: confirm this won't break piped input | |||
| final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath()).validationStringency(VALIDATION_STRINGENCY).open(SamInputResource.of(INPUT.toPath())); | |||
There was a problem hiding this comment.
@takutosato Could you put a comment here referencing this PR or the related issue? Just too save us some time when we forget and someone tries to change it.
|
@lbergelson yes the test fails when the workaround is removed. |
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Outdated suggestions cannot be applied.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
When we cloudify a Picard tool, we change the input and output file types from
FILEtoPicardHtsPath.This could trigger a "java.io.IOException: Illegal seek" if the input SAM is piped (/dev/stdin). I believe this is related to a known issue (see samtools/htsjdk#1084, samtools/htsjdk#1077). The workaround is to wrap a Path object inSamInputResource.of(), which was put in place in samtools/htsjdk#1124. The tests in PR should safeguard us from inadvertently removing the workaround until a more robust fix can be implemented.The targeted tools are RevertSam and MergeBamAlignment, both of which are used with piped input in warp pipelines. For example, see
https://github.com/broadinstitute/warp/blob/develop/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
https://github.com/broadinstitute/warp/blob/develop/tasks/broad/Alignment.wdl
To reproduce the bug, change Line 272 of RevertSam from:
to
That is, remove the wrapper
SamInputResource.of().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