{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/comments/45745344","id":45745344,"diff_hunk":"@@ -0,0 +1,43 @@\n+package org.broadinstitute.hellbender.tools.exome;\n+\n+import org.broadinstitute.hellbender.utils.Utils;\n+\n+/**\n+ * Enumeration of target annotations.\n+ * <p>\n+ *     A target annotation is a property of the target but not including the standard target name and coordinates.\n+ * </p>\n+ *\n+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;\n+ */\n+public enum TargetAnnotation {\n+\n+    /**\n+     * Fraction of bases that are G or C in the reference overlapping the target.\n+     *\n+     * <p>This value is always a number between 0 and 1 except in very rare cases with small targets with all, undefined bases (N or X),\n+     * in this case it value will be {@link Double#NaN NaN}</p>.\n+     */\n+    GC_BIAS(TargetTableColumn.GC_BIAS),","path":"src/main/java/org/broadinstitute/hellbender/tools/exome/TargetAnnotation.java","position":21,"original_position":21,"commit_id":"e28c1bc7e4d9c4414a0197cd1431cc5f2636f6c4","original_commit_id":"e28c1bc7e4d9c4414a0197cd1431cc5f2636f6c4","user":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars.githubusercontent.com/u/8438890?v=3","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"body":"CONTENT, not BIAS","created_at":"2015-11-24T14:59:12Z","updated_at":"2015-11-24T14:59:12Z","html_url":"https://github.com/broadinstitute/hellbender-protected/pull/190#discussion_r45745344","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/190","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/comments/45745344"},"html":{"href":"https://github.com/broadinstitute/hellbender-protected/pull/190#discussion_r45745344"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/190"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/190","id":51011993,"html_url":"https://github.com/broadinstitute/hellbender-protected/pull/190","diff_url":"https://github.com/broadinstitute/hellbender-protected/pull/190.diff","patch_url":"https://github.com/broadinstitute/hellbender-protected/pull/190.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/190","number":190,"state":"open","locked":false,"title":"(Don't merge before test pass) Adds a new tool to annotate targets with target specific properties.","user":{"login":"vruano","id":791104,"avatar_url":"https://avatars.githubusercontent.com/u/791104?v=3","gravatar_id":"","url":"https://api.github.com/users/vruano","html_url":"https://github.com/vruano","followers_url":"https://api.github.com/users/vruano/followers","following_url":"https://api.github.com/users/vruano/following{/other_user}","gists_url":"https://api.github.com/users/vruano/gists{/gist_id}","starred_url":"https://api.github.com/users/vruano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vruano/subscriptions","organizations_url":"https://api.github.com/users/vruano/orgs","repos_url":"https://api.github.com/users/vruano/repos","events_url":"https://api.github.com/users/vruano/events{/privacy}","received_events_url":"https://api.github.com/users/vruano/received_events","type":"User","site_admin":false},"body":"Adds a new tool to annotate targets with target specific properties.\r\n\r\nThis addresses issues #141 and #142.\r\n\r\nThe first two annotations supported are\r\n\r\n* GC_BIAS = Fraction of GC / Total number of sense bases in the target reference sequence.\r\n\r\n  - The user need to provide a reference.\r\n\r\n* REPEAT_FRACTION = Fraction of base in the target masked as repeated somewhere else in the referece.\r\n\r\n  - The user need to provide a BED file (indexed) with the repeated regions.\r\n\r\nAnnotations whose dependence is not provided won't be present in the output.\r\n\r\nSyntax:\r\n\r\n  java -jar hellbender-all.jar AnnotateTargets -R my-reference.fasta --repeats my-repeated-regions.bed -T targets.tab -o annotated-targets.tab\r\n\r\nThe output file will contain additional columns, one for each annotation with the corresponding value per each target in the input.\r\n\r\nOther changes:\r\n\r\n* Fixed an issue with progressMeter not being updated in the FeatureWalker.\r\n* Changed TargetColumn enum name to 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