Update radia.py for "samtools index" existence #12
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
During the process of applying your method, I found that the bam index for "xxx.bam" must be "xxx.bam.bai". However, my bam data came with "xxx.bai" format (created using Picard's BuildBamIndex) and cannot be modified (requires root privilege). I commented the "xxx.bam.bai" check code segments and the codes still worked (maybe samtools can auto-determine .bai or .bam.bai format). So I extended the bam index check codes to support both ".bam.bai" and ".bai" format.
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Outdated suggestions cannot be applied.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.
During the process of applying your method, I found that the bam index for "xxx.bam" must be "xxx.bam.bai". However, my bam data came with "xxx.bai" format (created using Picard's BuildBamIndex) and cannot be modified (requires root privilege).
I commented the "xxx.bam.bai" check code segments and the codes still worked (maybe samtools can auto-determine .bai or .bam.bai format).
So I extended the bam index check codes to support both ".bam.bai" and ".bai" format.