Skip indexing for bam_sort_stats_samtools
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Description
Samtools sort has been updated a while ago so that it can automatically add the index (crai/bai) of a bam file. I feel like the index step in the BAM_SORT_STATS_SAMTOOLS subworkflow is unneeded and can be replaced by taking an extra argument of the type of index you want and simply use the samtools sort to directly sort and index sam/bam files.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the BAM_SORT_STATS_SAMTOOLS subworkflow and reviewing how its separate index step currently follows Samtools sort. Check the Samtools sort behavior described in the issue, then update the subworkflow so the requested index type is passed as an argument and sorting produces the index directly. Done means the redundant index step is removed while SAM/BAM sorting and indexing still work.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100