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https://issues.apache.org/jira/browse/BEAM-2774?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16281015#comment-16281015
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ASF GitHub Bot commented on BEAM-2774:
--------------------------------------
jkff closed pull request #4221: [BEAM-2774] Remove a test case from VcfIO.
URL: https://github.com/apache/beam/pull/4221
This is a PR merged from a forked repository.
As GitHub hides the original diff on merge, it is displayed below for
the sake of provenance:
As this is a foreign pull request (from a fork), the diff is supplied
below (as it won't show otherwise due to GitHub magic):
diff --git a/sdks/python/apache_beam/io/vcfio_test.py
b/sdks/python/apache_beam/io/vcfio_test.py
index 7ff16d49b06..029515fe341 100644
--- a/sdks/python/apache_beam/io/vcfio_test.py
+++ b/sdks/python/apache_beam/io/vcfio_test.py
@@ -194,11 +194,6 @@ def _get_invalid_file_contents(self):
'#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT Sample\n',
'1 1 '
],
- # Missing "GT:GQ" format, but GQ is provided.
- [
- '#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT Sample\n',
- '19 123 rs12345 T C 50 q10
AF=0.2;NS=2 GT 1|0:48'
- ],
# GT is not an integer.
[
'#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT Sample\n',
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> Add I/O source for VCF files (python)
> -------------------------------------
>
> Key: BEAM-2774
> URL: https://issues.apache.org/jira/browse/BEAM-2774
> Project: Beam
> Issue Type: New Feature
> Components: sdk-py-core
> Reporter: Asha Rostamianfar
> Assignee: Miles Saul
> Original Estimate: 336h
> Remaining Estimate: 336h
>
> A new I/O source for reading (and eventually writing) VCF files [1] for
> Python. The design doc is available at
> https://docs.google.com/document/d/1jsdxOPALYYlhnww2NLURS8NKXaFyRSJrcGbEDpY9Lkw/edit
> [1] http://samtools.github.io/hts-specs/VCFv4.3.pdf
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