{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/48306471","id":48306471,"diff_hunk":"@@ -32,20 +32,31 @@\n     @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = \"Output metrics file.\")\n     public File OUTPUT;\n \n-    @Option(shortName = \"MQ\", doc = \"Minimum mapping quality for a read to contribute coverage.\", overridable = true)\n-    public int MINIMUM_MAPPING_QUALITY = 20;\n+    @Option(shortName = \"USABLE_MQ\", doc = \"Minimum mapping quality for a read to contribute to usable coverage.\", overridable = true)\n+    public int MINIMUM_USABLE_MAPPING_QUALITY = 20;\n \n-    @Option(shortName = \"Q\", doc = \"Minimum base quality for a base to contribute coverage.\", overridable = true)\n-    public int MINIMUM_BASE_QUALITY = 20;\n+    @Option(shortName = \"USABLE_Q\", doc = \"Minimum base quality for a base to contribute to usable coverage.\", overridable = true)\n+    public int MINIMUM_USABLE_BASE_QUALITY = 20;\n+\n+    @Option(shortName = \"RAW_MQ\", doc = \"Minimum mapping quality for a read to contribute to raw coverage.\", overridable = true)\n+    public int MINIMUM_RAW_MAPPING_QUALITY = 0;\n+\n+    @Option(shortName = \"RAW_Q\", doc = \"Minimum base quality for a base to contribute to raw coverage.\", overridable = true)\n+    public int MINIMUM_RAW_BASE_QUALITY = 3;\n \n     private final Log log = Log.getInstance(CollectWgsMetricsFromQuerySorted.class);\n \n+    public enum METRICS_TYPE { RAW, USABLE }\n+\n     /** Metrics for evaluating the performance of whole genome sequencing experiments. */\n     public static class QuerySortedSeqMetrics extends CollectWgsMetrics.WgsMetrics {\n+        /** Identifier for metrics type */\n+        public METRICS_TYPE TYPE;","path":"src/java/picard/analysis/CollectWgsMetricsFromQuerySorted.java","position":27,"original_position":27,"commit_id":"aaf815990f4cda298835e929c175261ee8b2ee2a","original_commit_id":"aaf815990f4cda298835e929c175261ee8b2ee2a","user":{"login":"eitanbanks","id":2751498,"avatar_url":"https://avatars.githubusercontent.com/u/2751498?v=3","gravatar_id":"","url":"https://api.github.com/users/eitanbanks","html_url":"https://github.com/eitanbanks","followers_url":"https://api.github.com/users/eitanbanks/followers","following_url":"https://api.github.com/users/eitanbanks/following{/other_user}","gists_url":"https://api.github.com/users/eitanbanks/gists{/gist_id}","starred_url":"https://api.github.com/users/eitanbanks/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eitanbanks/subscriptions","organizations_url":"https://api.github.com/users/eitanbanks/orgs","repos_url":"https://api.github.com/users/eitanbanks/repos","events_url":"https://api.github.com/users/eitanbanks/events{/privacy}","received_events_url":"https://api.github.com/users/eitanbanks/received_events","type":"User","site_admin":false},"body":"But we do call them raw and usable coverages - and we are keen to make those terms more widely used outside of the Broad...\r\n","created_at":"2015-12-22T22:38:12Z","updated_at":"2015-12-22T22:38:12Z","html_url":"https://github.com/broadinstitute/picard/pull/365#discussion_r48306471","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/365","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/48306471"},"html":{"href":"https://github.com/broadinstitute/picard/pull/365#discussion_r48306471"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/365"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/365","id":54393081,"html_url":"https://github.com/broadinstitute/picard/pull/365","diff_url":"https://github.com/broadinstitute/picard/pull/365.diff","patch_url":"https://github.com/broadinstitute/picard/pull/365.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/365","number":365,"state":"open","locked":false,"title":"Add capabilities to output both usable and raw metrics.","user":{"login":"eitanbanks","id":2751498,"avatar_url":"https://avatars.githubusercontent.com/u/2751498?v=3","gravatar_id":"","url":"https://api.github.com/users/eitanbanks","html_url":"https://github.com/eitanbanks","followers_url":"https://api.github.com/users/eitanbanks/followers","following_url":"https://api.github.com/users/eitanbanks/following{/other_user}","gists_url":"https://api.github.com/users/eitanbanks/gists{/gist_id}","starred_url":"https://api.github.com/users/eitanbanks/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eitanbanks/subscriptions","organizations_url":"https://api.github.com/users/eitanbanks/orgs","repos_url":"https://api.github.com/users/eitanbanks/repos","events_url":"https://api.github.com/users/eitanbanks/events{/privacy}","received_events_url":"https://api.github.com/users/eitanbanks/received_events","type":"User","site_admin":false},"body":"DO NOT MERGE.\r\n\r\nI'm still working on updating the tests.  But I wanted to get a quick code review from Yossi, Kathleen, and Jose given the time 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