{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/65571354","id":65571354,"diff_hunk":"@@ -77,10 +82,17 @@ public double sample(final Function<Double, Double> logPDF) {\n      * @param numBurnIn    number of samples to discard\n      * @return              samples drawn from the probability density function\n      */\n-    public List<Double> sample(final Function<Double, Double> logPDF, final int numSamples, final int numBurnIn) {\n+    public List<Double> sample(final RandomGenerator rng, final Function<Double, Double> logPDF, final int numSamples, final int numBurnIn) {\n+        Utils.nonNull(rng);\n+        Utils.nonNull(logPDF);\n+        ParamUtils.isPositive(numSamples, \"Number of samples must be positive.\");\n+        ParamUtils.isPositive(numBurnIn, \"Number of burn-in samples must be positive.\");\n+        if (numSamples < numBurnIn) {","path":"src/main/java/org/broadinstitute/hellbender/utils/mcmc/AdaptiveMetropolisSampler.java","position":72,"original_position":72,"commit_id":"983d53bfffcf4b9061f9f1e2484719cacbf47570","original_commit_id":"983d53bfffcf4b9061f9f1e2484719cacbf47570","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":"`Utils.validateArg(numBurnIn <= numSamples. . .)`","created_at":"2016-06-02T16:17:43Z","updated_at":"2016-06-02T16:17:43Z","html_url":"https://github.com/broadinstitute/gatk-protected/pull/534#discussion_r65571354","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/534","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/65571354"},"html":{"href":"https://github.com/broadinstitute/gatk-protected/pull/534#discussion_r65571354"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/534"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/534","id":72246186,"html_url":"https://github.com/broadinstitute/gatk-protected/pull/534","diff_url":"https://github.com/broadinstitute/gatk-protected/pull/534.diff","patch_url":"https://github.com/broadinstitute/gatk-protected/pull/534.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/534","number":534,"state":"open","locked":false,"title":"Refactored MCMC and copy-ratio model classes.","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":"-Parameters are now specified by an enum implementing the `ParameterEnum` interface rather than `String` names.  This obviates the need for some runtime checks that were performed by `AbstractParameterizedState` at the expense of needing to specify an additional parameterized type when defining samplers, models, etc.\r\n-Removed `AbstractParameterizedState` in favor of a concrete implementation `ParameterizedState<T extends Enum<T>, ParameterEnum>`, which can be subclassed with convenience getters to specify the state for a particular model.  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