{"action":"created","comment":{"url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/comments/193006763","pull_request_review_id":125889871,"id":193006763,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5MzAwNjc2Mw==","diff_hunk":"@@ -0,0 +1,80 @@\n+/*\n+ * Copyright 2018 EMBL - European Bioinformatics Institute\n+ *\n+ * Licensed under the Apache License, Version 2.0 (the \"License\");\n+ * you may not use this file except in compliance with the License.\n+ * You may obtain a copy of the License at\n+ *\n+ *      http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Unless required by applicable law or agreed to in writing, software\n+ * distributed under the License is distributed on an \"AS IS\" BASIS,\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n+ * See the License for the specific language governing permissions and\n+ * limitations under the License.\n+ */\n+package uk.ac.ebi.eva.accession.pipeline.steps.tasklets.reportCheck;\n+\n+import uk.ac.ebi.eva.commons.core.models.VariantCoreFields;\n+import uk.ac.ebi.eva.commons.core.models.factories.VariantVcfFactory;\n+import uk.ac.ebi.eva.commons.core.models.factories.exception.IncompleteInformationException;\n+import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;\n+import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;\n+import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;\n+\n+import java.util.Arrays;\n+import java.util.Collections;\n+import java.util.HashSet;\n+import java.util.LinkedList;\n+import java.util.List;\n+import java.util.Set;\n+\n+/**\n+ * Transforms a String (in VCF format) to a list of variants, keeping only the basic fields (coordinates):\n+ * chromosome, position, id, reference, alternate.\n+ */\n+public class CoordinatesVcfFactory extends VariantVcfFactory {","path":"eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/steps/tasklets/reportCheck/CoordinatesVcfFactory.java","position":36,"original_position":36,"commit_id":"0a118ee4e26a19caff2de95c81f07334dd276700","original_commit_id":"0a118ee4e26a19caff2de95c81f07334dd276700","user":{"login":"jmmut","id":4750555,"node_id":"MDQ6VXNlcjQ3NTA1NTU=","avatar_url":"https://avatars3.githubusercontent.com/u/4750555?v=4","gravatar_id":"","url":"https://api.github.com/users/jmmut","html_url":"https://github.com/jmmut","followers_url":"https://api.github.com/users/jmmut/followers","following_url":"https://api.github.com/users/jmmut/following{/other_user}","gists_url":"https://api.github.com/users/jmmut/gists{/gist_id}","starred_url":"https://api.github.com/users/jmmut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmmut/subscriptions","organizations_url":"https://api.github.com/users/jmmut/orgs","repos_url":"https://api.github.com/users/jmmut/repos","events_url":"https://api.github.com/users/jmmut/events{/privacy}","received_events_url":"https://api.github.com/users/jmmut/received_events","type":"User","site_admin":false},"body":"I don't think so because it wouldn't reject non-variants and would accession them","created_at":"2018-06-05T09:33:04Z","updated_at":"2018-06-05T09:33:04Z","html_url":"https://github.com/EBIvariation/eva-accession/pull/19#discussion_r193006763","pull_request_url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/19","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/comments/193006763"},"html":{"href":"https://github.com/EBIvariation/eva-accession/pull/19#discussion_r193006763"},"pull_request":{"href":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/19"}},"in_reply_to_id":191810492},"pull_request":{"url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/19","id":189039951,"node_id":"MDExOlB1bGxSZXF1ZXN0MTg5MDM5OTUx","html_url":"https://github.com/EBIvariation/eva-accession/pull/19","diff_url":"https://github.com/EBIvariation/eva-accession/pull/19.diff","patch_url":"https://github.com/EBIvariation/eva-accession/pull/19.patch","issue_url":"https://api.github.com/repos/EBIvariation/eva-accession/issues/19","number":19,"state":"open","locked":false,"title":"EVA-1204 Post-accessioning validation checks (2/2)","user":{"login":"jmmut","id":4750555,"node_id":"MDQ6VXNlcjQ3NTA1NTU=","avatar_url":"https://avatars3.githubusercontent.com/u/4750555?v=4","gravatar_id":"","url":"https://api.github.com/users/jmmut","html_url":"https://github.com/jmmut","followers_url":"https://api.github.com/users/jmmut/followers","following_url":"https://api.github.com/users/jmmut/following{/other_user}","gists_url":"https://api.github.com/users/jmmut/gists{/gist_id}","starred_url":"https://api.github.com/users/jmmut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmmut/subscriptions","organizations_url":"https://api.github.com/users/jmmut/orgs","repos_url":"https://api.github.com/users/jmmut/repos","events_url":"https://api.github.com/users/jmmut/events{/privacy}","received_events_url":"https://api.github.com/users/jmmut/received_events","type":"User","site_admin":false},"body":"requires https://github.com/EBIvariation/variation-commons/pull/71\r\n\r\nI still have to do a manual run to check that everything is wired properly, but the review can already be done.\r\n\r\nNote that there are several ways the VCF comparison could be done. The one here tries to avoid loading the whole input VCF in memory, by loading only a chunk. In most executions this will be enough, but if the report VCF is unordered in the absolute worst way, the report VCF may be completely loaded in memory.","created_at":"2018-05-18T14:16:10Z","updated_at":"2018-06-05T09:33:04Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d6ae83cd072452d7209d944763e6587fde683dc8","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/19/commits","review_comments_url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/19/comments","review_comment_url":"https://api.github.com/repos/EBIvariation/eva-accession/pulls/comments{/number}","comments_url":"https://api.github.com/repos/EBIvariation/eva-accession/issues/19/comments","statuses_url":"https://api.github.com/repos/EBIvariation/eva-accession/statuses/0a118ee4e26a19caff2de95c81f07334dd276700","head":{"label":"jmmut:feature/compare-vcfs","ref":"feature/compare-vcfs","sha":"0a118ee4e26a19caff2de95c81f07334dd276700","user":{"login":"jmmut","id":4750555,"node_id":"MDQ6VXNlcjQ3NTA1NTU=","avatar_url":"https://avatars3.githubusercontent.com/u/4750555?v=4","gravatar_id":"","url":"https://api.github.com/users/jmmut","html_url":"https://github.com/jmmut","followers_url":"https://api.github.com/users/jmmut/followers","following_url":"https://api.github.com/users/jmmut/following{/other_user}","gists_url":"https://api.github.com/users/jmmut/gists{/gist_id}","starred_url":"https://api.github.com/users/jmmut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmmut/subscriptions","organizations_url":"https://api.github.com/users/jmmut/orgs","repos_url":"https://api.github.com/users/jmmut/repos","events_url":"https://api.github.com/users/jmmut/events{/privacy}","received_events_url":"https://api.github.com/users/jmmut/received_events","type":"User","site_admin":false},"repo":{"id":126814091,"node_id":"MDEwOlJlcG9zaXRvcnkxMjY4MTQwOTE=","name":"eva-accession","full_name":"jmmut/eva-accession","owner":{"login":"jmmut","id":4750555,"node_id":"MDQ6VXNlcjQ3NTA1NTU=","avatar_url":"https://avatars3.githubusercontent.com/u/4750555?v=4","gravatar_id":"","url":"https://api.github.com/users/jmmut","html_url":"https://github.com/jmmut","followers_url":"https://api.github.com/users/jmmut/followers","following_url":"https://api.github.com/users/jmmut/following{/other_user}","gists_url":"https://api.github.com/users/jmmut/gists{/gist_id}","starred_url":"https://api.github.com/users/jmmut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmmut/subscriptions","organizations_url":"https://api.github.com/users/jmmut/orgs","repos_url":"https://api.github.com/users/jmmut/repos","events_url":"https://api.github.com/users/jmmut/events{/privacy}","received_events_url":"https://api.github.com/users/jmmut/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jmmut/eva-accession","description":"EVA 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