{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/29780225","id":29780225,"diff_hunk":"@@ -565,6 +592,39 @@ static SplitLocusRecursive splitLocusIntervals1(LinkedList<GenomeLoc> remaining,\n         return new SplitLocusRecursive(split, remaining);\n     }\n \n+    /**\n+     * Check whether to locatable overlap.\n+     * <p>\n+     *    Two locatables overlap if the share the same contig and they have at least one\n+     *    base in common based on their start and end positions.\n+     * </p>\n+     * <p>\n+     *    This method returns {@code false} if either input {@link Locatable} has a {@code null}\n+     *    contig.\n+     * </p>\n+     *\n+     * @param left first locatable.\n+     * @param right second locatable.\n+     * @throws IllegalArgumentException if either {@code left} or {@code right} locatable\n+     *  is {@code null}.\n+     * @return {@code true} iff there is an overlap between both locatables.\n+     */\n+    public static boolean overlaps(final Locatable left,final Locatable right) {\n+        Utils.nonNull(left,\"the left locatable is null\");\n+        Utils.nonNull(right,\"the right locatable is null\");\n+        if (left.getContig() == null || right.getContig() == null) {\n+            return false;\n+        } else if (!left.getContig().equals(right.getContig())) {\n+            return false;\n+        } else {\n+            // If there is no overlap the cross-differences between\n+            // start and ends should both either be positive or negative;\n+            // never mixed or zero.\n+            return Integer.compare(left.getStart(),right.getEnd()) *\n+                    Integer.compare(left.getEnd(),right.getStart()) <= 0;","path":"src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java","position":76,"original_position":76,"commit_id":"9aefdd5883ef96dfb6ace6e85ef5a08a6ea1baa1","original_commit_id":"9aefdd5883ef96dfb6ace6e85ef5a08a6ea1baa1","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":"Oups you right! thanks.","created_at":"2015-05-06T17:17:28Z","updated_at":"2015-05-06T17:17:28Z","html_url":"https://github.com/broadinstitute/hellbender/pull/483#discussion_r29780225","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/483","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/29780225"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/483#discussion_r29780225"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/483"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/483","id":34595910,"html_url":"https://github.com/broadinstitute/hellbender/pull/483","diff_url":"https://github.com/broadinstitute/hellbender/pull/483.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/483.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/483","number":483,"state":"open","locked":false,"title":"Adds the possibility of specifying exons using a separate BED file.","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":"The BED file would contain names for each exon. 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