Auto-Save Index Files Alongside BAMs #446
Open
+15,479
−82
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
Some small optimizations too.
…ally too large to benefit from Steve's ComputeAllowedLocalSSD optimization.
…and conversion to .g.vcf.bgz steps
- Local disk to SSD
- samtools index -@ 2 ~{basename(prefix)}
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
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Outdated suggestions cannot be applied.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.
Overview:
This branch is built on top of jts_kvg_sp_malaria branch. This PR improves our BAM file indexing process by ensuring index files are automatically saved alongside BAM files.
Key Updates:
outdirparameter inSRIndexBamworkflow is now optional. The workflow places.baifiles next to their.bamfiles ifoutdirisn't provided.Adjusted
FinalizeBamIndexto automatically detect and use the BAM file directory for storing.baifiles.Benefits:
Ensures .bai files are easily accessible for analysis.
Testing:
Tests confirm correct
.baifile placement in specified and derivedoutdircases, ensuring reliability across various scenarios.