Read bam with split reads
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
- No merged PRs in 30d
Description
Hi, first of all thanks a lot for this great tool!
I was wondering if it would be possible to have the make fragment files function from bam files also consider split reads in addition to clipped reads? Do you think this would be difficult to implement?
Thanks a lot for your help!
Contributor guide
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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
Locate the function that creates fragment files from BAM files and inspect how it currently handles clipped reads. Determine how split reads should be recognized and included alongside them. Done means fragment files produced from BAM input include the requested split reads, with behavior checked against the existing clipped-read handling.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100