{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/70832837","id":70832837,"diff_hunk":"@@ -60,6 +62,44 @@ public AllelicCount(final SimpleInterval interval, final int refReadCount, final\n         this(interval, refReadCount, altReadCount, refNucleotide, altNucleotide, readDepth, null);\n     }\n \n+    public AllelicCount(final AllelicCount count) {\n+        this.interval = count.getInterval();\n+        this.refReadCount = count.getRefReadCount();\n+        this.altReadCount = count.getAltReadCount();\n+\n+        //if fields in original AllelicCount are null, getters throw IllegalArgumentExceptions; catch these and set fields in copy to null\n+        Nucleotide tempNucleotide;\n+        try {\n+            tempNucleotide = count.getRefNucleotide();\n+        } catch (final IllegalArgumentException e) {\n+            tempNucleotide = null;\n+        }\n+        this.refNucleotide = tempNucleotide;\n+\n+        try {\n+            tempNucleotide = count.getAltNucleotide();\n+        } catch (final IllegalArgumentException e) {\n+            tempNucleotide = null;\n+        }\n+        this.altNucleotide = tempNucleotide;\n+\n+        Integer tempInteger;\n+        try {\n+            tempInteger = count.getReadDepth();\n+        } catch (final IllegalArgumentException e) {\n+            tempInteger = null;\n+        }\n+        this.readDepth = tempInteger;\n+\n+        Double tempDouble;\n+        try {","path":"src/main/java/org/broadinstitute/hellbender/tools/exome/alleliccount/AllelicCount.java","position":60,"original_position":60,"commit_id":"71005b295133777e22959ca227ccfae25c28bca1","original_commit_id":"f7cdf9459d1d5d34bd6213c814845c28f8c085a7","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":"Similarly, why not `this.hetLogOdds = count.hetLogOdds`?","created_at":"2016-07-14T16:01:23Z","updated_at":"2016-07-14T16:01:23Z","html_url":"https://github.com/broadinstitute/gatk-protected/pull/574#discussion_r70832837","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/574","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/70832837"},"html":{"href":"https://github.com/broadinstitute/gatk-protected/pull/574#discussion_r70832837"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/574"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/574","id":74472769,"html_url":"https://github.com/broadinstitute/gatk-protected/pull/574","diff_url":"https://github.com/broadinstitute/gatk-protected/pull/574.diff","patch_url":"https://github.com/broadinstitute/gatk-protected/pull/574.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/574","number":574,"state":"open","locked":false,"title":"Added CalculatePulldownPhasePosteriors.","user":{"login":"samuelklee","id":11076296,"avatar_url":"https://avatars.githubusercontent.com/u/11076296?v=3","gravatar_id":"","url":"https://api.github.com/users/samuelklee","html_url":"https://github.com/samuelklee","followers_url":"https://api.github.com/users/samuelklee/followers","following_url":"https://api.github.com/users/samuelklee/following{/other_user}","gists_url":"https://api.github.com/users/samuelklee/gists{/gist_id}","starred_url":"https://api.github.com/users/samuelklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samuelklee/subscriptions","organizations_url":"https://api.github.com/users/samuelklee/orgs","repos_url":"https://api.github.com/users/samuelklee/repos","events_url":"https://api.github.com/users/samuelklee/events{/privacy}","received_events_url":"https://api.github.com/users/samuelklee/received_events","type":"User","site_admin":false},"body":"Also:\r\n-Created AllelicCount package and added 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