galaxyproject / galaxyproject/galaxy

when upload sorted bam file to usegalay -> automated changing unsorted bam

Open
#16,635 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
1.9k
Forks
1.2k
Avg merge
2d 16h
Merged PRs (30d)
169

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

Open the contributing 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.