{"action":"created","comment":{"url":"https://api.github.com/repos/molgenis/gavin-plus/pulls/comments/197347712","pull_request_review_id":131074656,"id":197347712,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5NzM0NzcxMg==","diff_hunk":"@@ -1,69 +1,102 @@\n package org.molgenis.data.annotation.makervcf;\n \n+import org.apache.commons.lang3.StringUtils;\n import org.molgenis.calibratecadd.support.GavinUtils;\n import org.molgenis.data.annotation.makervcf.structs.GavinRecord;\n import org.molgenis.vcf.VcfReader;\n import org.molgenis.vcf.VcfWriter;\n import org.molgenis.vcf.VcfWriterFactory;\n import org.molgenis.vcf.meta.VcfMeta;\n import org.molgenis.vcf.meta.VcfMetaInfo;\n+import org.slf4j.Logger;\n+import org.slf4j.LoggerFactory;\n \n import java.io.File;\n import java.io.IOException;\n import java.util.*;\n \n-/**\n- * Created by joeri on 7/18/16.\n- */\n+import static org.molgenis.data.annotation.makervcf.structs.RVCF.*;\n+\n class WriteToRVCF\n {\n-\tvoid writeRVCF(Iterator<GavinRecord> relevantVariants, File writeTo, File inputVcfFile, boolean writeToDisk,\n-\t\t\tboolean verbose) throws Exception\n+\tprivate static final Logger LOG = LoggerFactory.getLogger(WriteToRVCF.class);\n+\tpublic static final String STRING = \"String\";\n+\n+\tvoid writeRVCF(Iterator<GavinRecord> gavinRecords, File writeTo, File inputVcfFile, String version,\n+\t\t\tString cmdString, boolean writeToDisk, boolean splitRlvField, boolean includeSamples) throws Exception","path":"src/main/java/org/molgenis/data/annotation/makervcf/WriteToRVCF.java","position":31,"original_position":31,"commit_id":"8aa2043e54fc36098a7b722d6d44b418b24f9d21","original_commit_id":"8aa2043e54fc36098a7b722d6d44b418b24f9d21","user":{"login":"molgenis-jenkins","id":15369941,"node_id":"MDQ6VXNlcjE1MzY5OTQx","avatar_url":"https://avatars2.githubusercontent.com/u/15369941?v=4","gravatar_id":"","url":"https://api.github.com/users/molgenis-jenkins","html_url":"https://github.com/molgenis-jenkins","followers_url":"https://api.github.com/users/molgenis-jenkins/followers","following_url":"https://api.github.com/users/molgenis-jenkins/following{/other_user}","gists_url":"https://api.github.com/users/molgenis-jenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/molgenis-jenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/molgenis-jenkins/subscriptions","organizations_url":"https://api.github.com/users/molgenis-jenkins/orgs","repos_url":"https://api.github.com/users/molgenis-jenkins/repos","events_url":"https://api.github.com/users/molgenis-jenkins/events{/privacy}","received_events_url":"https://api.github.com/users/molgenis-jenkins/received_events","type":"User","site_admin":false},"body":"![MAJOR](https://sonarsource.github.io/sonar-github/severity-major.png 'Severity: MAJOR') Define and throw a dedicated exception instead of using a generic one. [![rule](https://sonarsource.github.io/sonar-github/rule.png)](https://sonarcloud.io/coding_rules#rule_key=squid%3AS00112)\n","created_at":"2018-06-22T06:00:33Z","updated_at":"2018-06-22T06:00:33Z","html_url":"https://github.com/molgenis/gavin-plus/pull/51#discussion_r197347712","pull_request_url":"https://api.github.com/repos/molgenis/gavin-plus/pulls/51","author_association":"NONE","_links":{"self":{"href":"https://api.github.com/repos/molgenis/gavin-plus/pulls/comments/197347712"},"html":{"href":"https://github.com/molgenis/gavin-plus/pull/51#discussion_r197347712"},"pull_request":{"href":"https://api.github.com/repos/molgenis/gavin-plus/pulls/51"}}},"pull_request":{"url":"https://api.github.com/repos/molgenis/gavin-plus/pulls/51","id":195434947,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk1NDM0OTQ3","html_url":"https://github.com/molgenis/gavin-plus/pull/51","diff_url":"https://github.com/molgenis/gavin-plus/pull/51.diff","patch_url":"https://github.com/molgenis/gavin-plus/pull/51.patch","issue_url":"https://api.github.com/repos/molgenis/gavin-plus/issues/51","number":51,"state":"open","locked":false,"title":"M5900 Cli options and various improvements","user":{"login":"dennishendriksen","id":2477186,"node_id":"MDQ6VXNlcjI0NzcxODY=","avatar_url":"https://avatars1.githubusercontent.com/u/2477186?v=4","gravatar_id":"","url":"https://api.github.com/users/dennishendriksen","html_url":"https://github.com/dennishendriksen","followers_url":"https://api.github.com/users/dennishendriksen/followers","following_url":"https://api.github.com/users/dennishendriksen/following{/other_user}","gists_url":"https://api.github.com/users/dennishendriksen/gists{/gist_id}","starred_url":"https://api.github.com/users/dennishendriksen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dennishendriksen/subscriptions","organizations_url":"https://api.github.com/users/dennishendriksen/orgs","repos_url":"https://api.github.com/users/dennishendriksen/repos","events_url":"https://api.github.com/users/dennishendriksen/events{/privacy}","received_events_url":"https://api.github.com/users/dennishendriksen/received_events","type":"User","site_admin":false},"body":"- Command line option -k: Do not filter the non relevant variants, return all variants from the input\r\n- Command line option -s: Include samples in output\r\n- Command line option -q: Create separate INFO fields for every part of the RLV information\r\n- #15 Add GavinVersion and GavinCmd headers to output VCF\r\n- Remove standalone mergeback tool\r\n- Remove standalone split RLV tool\r\n- Logging improvements\r\n- Code quality 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