{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/38923676","id":38923676,"diff_hunk":"@@ -52,14 +52,25 @@\n  * @author Tim Fennell\n  */\n @CommandLineProgramProperties(\n-        usage = \"Program to generate a data table and pdf chart of \" +\n-                \"mean base quality by cycle from a SAM or BAM file.  Works best on a single lane/run of data, but can be applied to\" +\n-                \"merged BAMs. Uses R to generate chart output.\",\n-        usageShort = \"Writes mean quality by cycle for a SAM or BAM file\",\n+        usage = MeanQualityByCycle.USAGE_SUMMARY + MeanQualityByCycle.USAGE_DETAILS,\n+        usageShort = MeanQualityByCycle.USAGE_SUMMARY,\n         programGroup = Metrics.class\n )\n public class MeanQualityByCycle extends SinglePassSamProgram {\n-\n+    static final String USAGE_SUMMARY = \"Writes mean quality by cycle for a SAM or BAM file\";\n+    static final String USAGE_DETAILS = \"Tool generates a data table and chart of mean quality by cycle from a BAM file.\" +\n+            \"  Works best on a single lane/run of data, but can be applied to merged BAMs.  <br /><br />\" +\n+            \"This metric gives an overall snapshot of sequencing machine performance, as base quality scores\" +\n+            \" tend to decrease towards the end of a run. <br /><br />\" +\n+            \"\" +","path":"src/java/picard/analysis/MeanQualityByCycle.java","position":19,"original_position":19,"commit_id":"d3e1c4a832985aec8fb9004daf5b64edf7bbdcd4","original_commit_id":"d3e1c4a832985aec8fb9004daf5b64edf7bbdcd4","user":{"login":"ktibbett","id":3082072,"avatar_url":"https://avatars.githubusercontent.com/u/3082072?v=3","gravatar_id":"","url":"https://api.github.com/users/ktibbett","html_url":"https://github.com/ktibbett","followers_url":"https://api.github.com/users/ktibbett/followers","following_url":"https://api.github.com/users/ktibbett/following{/other_user}","gists_url":"https://api.github.com/users/ktibbett/gists{/gist_id}","starred_url":"https://api.github.com/users/ktibbett/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ktibbett/subscriptions","organizations_url":"https://api.github.com/users/ktibbett/orgs","repos_url":"https://api.github.com/users/ktibbett/repos","events_url":"https://api.github.com/users/ktibbett/events{/privacy}","received_events_url":"https://api.github.com/users/ktibbett/received_events","type":"User","site_admin":false},"body":"Two separate sentences?  \r\n\"This metric gives an overall snapshot of sequencing machine performance.  Base quality scores\" +\r\n+            \" tend to decrease towards the end of a run. <br /><br />\" +","created_at":"2015-09-08T13:19:58Z","updated_at":"2015-09-08T13:19:58Z","html_url":"https://github.com/broadinstitute/picard/pull/230#discussion_r38923676","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/230","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/38923676"},"html":{"href":"https://github.com/broadinstitute/picard/pull/230#discussion_r38923676"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/230"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/230","id":39490546,"html_url":"https://github.com/broadinstitute/picard/pull/230","diff_url":"https://github.com/broadinstitute/picard/pull/230.diff","patch_url":"https://github.com/broadinstitute/picard/pull/230.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/230","number":230,"state":"open","locked":false,"title":"Improved documentation for Picard 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