Added compressed parameter to read_10x_mtx to support STARsolo output #3564
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I noticed the CI check for milestone is failing. As a new contributor, I don't seem to have permissions to add labels. Could a maintainer please add the appropriate milestone or "no milestone" label? Thank you! |
Zethson
reviewed
Apr 8, 2025
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The test failures are unrelated, no worries. |
Zethson
reviewed
Apr 9, 2025
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I didn't really see any tests related to the different versions and them being compressed. I think a test in https://github.com/scverse/scanpy/blob/main/tests/test_read_10x.py would be beneficial.
Could you please also add a release note?
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Let me know if anything else is needed. |
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Thanks! |
selmanozleyen
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Apr 14, 2025
…scverse#3564) Co-authored-by: MacBook Air <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Description
This PR adds a new
compressedparameter to theread_10x_mtxfunction to support reading uncompressed matrix files produced by tools like STARsolo.The current implementation assumes all Cell Ranger v3+ files are gzipped (.gz), forcing users to compress STARsolo output files unnecessarily before using them with Scanpy.
Changes
compressedparameter (default: True) toread_10x_mtx_read_10x_mtxfunction to respect this parameter