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https://issues.apache.org/jira/browse/BEAM-2774?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16271673#comment-16271673
]
ASF GitHub Bot commented on BEAM-2774:
--------------------------------------
chamikaramj commented on a change in pull request #4157: [BEAM-2774] Added
loose failure mode to allow individual VCF record reads to fail
URL: https://github.com/apache/beam/pull/4157#discussion_r153935841
##########
File path: sdks/python/apache_beam/io/vcfio.py
##########
@@ -274,7 +285,9 @@ def __init__(self,
try:
self._vcf_reader = vcf.Reader(fsock=self._create_generator())
except SyntaxError as e:
- raise ValueError('Invalid VCF header %s' % str(e))
+ raise ValueError('An exception was raised when reading header from VCF
'
Review comment:
<!--new_thread; commit:7f28b9aa6b0f1e5d4b1ef2ed0cb1a97249db9b70;
resolved:0-->
How about following (without using new lines).
'An exception was raised when reading header from VCF file %s: %s'
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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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