Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 71088200D48 for ; Wed, 29 Nov 2017 23:35:05 +0100 (CET) Received: by cust-asf.ponee.io (Postfix) id 6F6F0160C16; Wed, 29 Nov 2017 22:35:05 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id B6D94160C04 for ; Wed, 29 Nov 2017 23:35:04 +0100 (CET) Received: (qmail 51672 invoked by uid 500); 29 Nov 2017 22:35:03 -0000 Mailing-List: contact commits-help@beam.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@beam.apache.org Delivered-To: mailing list commits@beam.apache.org Received: (qmail 51663 invoked by uid 99); 29 Nov 2017 22:35:03 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd3-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 29 Nov 2017 22:35:03 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd3-us-west.apache.org (ASF Mail Server at spamd3-us-west.apache.org) with ESMTP id 5ED6D180933 for ; Wed, 29 Nov 2017 22:35:03 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd3-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: -99.202 X-Spam-Level: X-Spam-Status: No, score=-99.202 tagged_above=-999 required=6.31 tests=[KAM_ASCII_DIVIDERS=0.8, RP_MATCHES_RCVD=-0.001, SPF_PASS=-0.001, USER_IN_WHITELIST=-100] autolearn=disabled Received: from mx1-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd3-us-west.apache.org [10.40.0.10]) (amavisd-new, port 10024) with ESMTP id lw0tSCOSOvHA for ; Wed, 29 Nov 2017 22:35:02 +0000 (UTC) Received: from mailrelay1-us-west.apache.org (mailrelay1-us-west.apache.org [209.188.14.139]) by mx1-lw-eu.apache.org (ASF Mail Server at mx1-lw-eu.apache.org) with ESMTP id D9BC25F286 for ; Wed, 29 Nov 2017 22:35:01 +0000 (UTC) Received: from jira-lw-us.apache.org (unknown [207.244.88.139]) by mailrelay1-us-west.apache.org (ASF Mail Server at mailrelay1-us-west.apache.org) with ESMTP id 23E20E0662 for ; Wed, 29 Nov 2017 22:35:01 +0000 (UTC) Received: from jira-lw-us.apache.org (localhost [127.0.0.1]) by jira-lw-us.apache.org (ASF Mail Server at jira-lw-us.apache.org) with ESMTP id D578C21058 for ; Wed, 29 Nov 2017 22:35:00 +0000 (UTC) Date: Wed, 29 Nov 2017 22:35:00 +0000 (UTC) From: "ASF GitHub Bot (JIRA)" To: commits@beam.apache.org Message-ID: In-Reply-To: References: Subject: [jira] [Commented] (BEAM-2774) Add I/O source for VCF files (python) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-JIRA-FingerPrint: 30527f35849b9dde25b450d4833f0394 archived-at: Wed, 29 Nov 2017 22:35:05 -0000 [ https://issues.apache.org/jira/browse/BEAM-2774?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16271674#comment-16271674 ] 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_r153935838 ########## File path: sdks/python/apache_beam/io/vcfio.py ########## @@ -427,10 +452,17 @@ def __init__( underlying file_path's extension will be used to detect the compression. validate (bool): flag to verify that the files exist during the pipeline creation time. + allow_malformed_records (bool): Determines if failed VCF Review comment: s/Determines/determines ---------------------------------------------------------------- This is an automated message from the Apache Git Service. To respond to the message, please log on GitHub and use the URL above to go to the specific comment. For queries about this service, please contact Infrastructure at: users@infra.apache.org > 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 -- This message was sent by Atlassian JIRA (v6.4.14#64029)