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https://issues.apache.org/jira/browse/BEAM-2774?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16261362#comment-16261362
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ASF GitHub Bot commented on BEAM-2774:
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GitHub user mhsaul opened a pull request:
https://github.com/apache/beam/pull/4157
[BEAM-2774] Added loose failure mode to allow individual VCF record reads
to fail
Added configuration parameter `allow_malformed_records` that allows reads
for records to be logged and returned as `MalformedVcfRecord` objects so that
the pipeline can continue if some records are malformed.
@chamikaramj, @jkff can you please take a look?
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/mhsaul/beam vcf-record-loose-mode
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/beam/pull/4157.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #4157
----
commit b46a3e7e83af5e45d1dd520f22db5bb155f760b3
Author: Miles Saul <[email protected]>
Date: 2017-11-21T19:30:16Z
Added loose failure mode to allow individual VCF record reads to fail
----
> 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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