{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/63913745","id":63913745,"diff_hunk":"@@ -0,0 +1,44 @@\n+package org.broadinstitute.hellbender.utils;\n+\n+import htsjdk.tribble.Tribble;\n+import htsjdk.tribble.index.Index;\n+import htsjdk.tribble.index.IndexFactory;\n+import org.apache.logging.log4j.LogManager;\n+import org.apache.logging.log4j.Logger;\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+\n+import java.io.File;\n+\n+public final class IndexUtils {\n+    private IndexUtils(){}\n+\n+    private static final Logger logger = LogManager.getLogger(IndexUtils.class);\n+\n+    /**\n+     * Load the index from disk, checking for out of date indexes and old versions\n+     * @return an Index, or null if we're unable to load\n+     */\n+    public static Index loadTribbleIndex(final File featureFile) {\n+        Utils.nonNull(featureFile);\n+        final File indexFile = Tribble.indexFile(featureFile);\n+        if (! indexFile.canRead()) {\n+            return null;\n+        }\n+        logger.debug(\"Loading Tribble index from disk for file \" + featureFile);\n+        final Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());\n+        checkIndexModificationTime(featureFile, indexFile, index);\n+        return index;\n+    }\n+\n+    /**\n+     * @throws UserException the index not up-to date (ie older than the feature file) and is not the current 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incompatible sequence dictionaries.","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"Use SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH to indicate missing length.\r\n\r\nfixes https://github.com/broadinstitute/gatk/issues/1029\r\n\r\n@droazen please review","created_at":"2016-01-08T21:09:45Z","updated_at":"2016-05-19T16:46:15Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f7ab1f019ce971bf810ce68dd5f323dbab6b130e","assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1425/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1425/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1425/comments","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/e0bb2dc47b787726e018cf54a67b31c548400c8a","head":{"label":"broadinstitute:ak_featureSeqDictFromIndex","ref":"ak_featureSeqDictFromIndex","sha":"e0bb2dc47b787726e018cf54a67b31c548400c8a","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"gatk","full_name":"broadinstitute/gatk","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/gatk","description":"GATK4 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