galaxyproject / galaxyproject/galaxy
when upload sorted bam file to usegalay -> automated changing unsorted bam
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- Dominant language
- Python
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Description
When I upload a sorted bam file to galaxy, it is automatically registered as an unsorted bam. The header of the bam file already contains SO:coordinate, but how can I get it automatically converted to an unsorted bam? I tried to use the converter in the attribute, but I get an error that it is a truncated file.
Contributor guide
Research direction
No files, tests, or entry points are named. Start by reproducing the sorted BAM upload in Galaxy and inspect the converter error for the truncated-file report. Done means the upload preserves or correctly handles the BAM sort status, with coverage for the reported case.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100