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Read10x updates #88

Merged
merged 2 commits into from
Oct 22, 2024
Merged

Read10x updates #88

merged 2 commits into from
Oct 22, 2024

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Nick-Eagles
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All changes modify read10xVisiumWrapper() to allow finding and importing the reference GTF properly, namely when reference_gtf is not specified. In particular:

  • Correctly find the reference GTF for recent versions of spaceranger, which have a differently organized web_summary.html file
  • Support importing GTF files that are gzipped, which occurs for recent reference genomes (such as those from 2024)

Nick-Eagles and others added 2 commits October 11, 2024 11:14
@Nick-Eagles @manishabarse
Support finding the reference GTF properly even for spaceranger versi…
ed85b26 
…ons > 3.0.0

Co-authored-by: Manisha Barse <mbarse.libd@gmail.com>
@Nick-Eagles
Support automatically importing gzip'd GTF files, which occur in the …
e2001c6 
…recent annotation files (e.g. 2024)
@lcolladotor lcolladotor merged commit 107929e into LieberInstitute:devel Oct 22, 2024
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lcolladotor added a commit that referenced this pull request Oct 22, 2024
@lcolladotor
v1.17.9 -- document #88 by @Nick-Eagles
97dffb7
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@Nick-Eagles @lcolladotor