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The classification is based on a heuristic that was derived by looking at a few titration experiments.\",\n-        usageShort = \"Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.\",\n+        usage = CollectHiSeqXPfFailMetrics.USAGE_SUMMARY + CollectHiSeqXPfFailMetrics.USAGE_DETAILS,\n+        usageShort = CollectHiSeqXPfFailMetrics.USAGE_SUMMARY,\n         programGroup = Metrics.class\n )\n \n public class CollectHiSeqXPfFailMetrics extends CommandLineProgram {\n+    static final String USAGE_SUMMARY = \"Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.\";\n+    static final String USAGE_DETAILS = \"<p>This tool categorizes the reads that did not pass filter (PF-Failing) into four \" +\n+            \"groups.  These groups are based on a heuristic that was derived by looking at a few titration experiments. </p>\" +\n+            \"\" +\n+            \"<p>After examining the called bases from the first 24 cycles of each read, the PF-Failed reads are grouped into the \" +\n+            \"following four categories: \" +\n+            \"<ul>\" +\n+            \"<li>MISALIGNED - The first 24 basecalls of a read are uncalled (numNs~24).  \" +\n+            \" These types of reads appear to be flow cell artifacts because reads \" +\n+            \"were only found near tile boundaries and were concentration (library) independent</li> \" +\n+            \"<li>Empty wells - All 24 bases are called (numNs~0) but the number of bases with quality scores\" +\n+            \" greater than two is less than or equal to eight (numQGtTwo<=8).  These reads were location independent within the tiles and \" +\n+            \"were inversely proportional to the library concentration</li>\" +\n+            \"\" +\n+            \"<li>Polyclonal wells - All 24 bases were called and numQGtTwo>=12, were independent of their location with the tiles, \" +\n+            \"and were directly proportional to the library concentration.  These reads are likely the result of PCR artifacts </li>\" +\n+            \"<li>UNKNOWN - The remaining reads that PF-Failing but did not fit into any of the groups listed above</li>\"   +","path":"src/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java","position":28,"original_position":28,"commit_id":"0d272d6a62d27498fe7f3fac94529cf41d7f405d","original_commit_id":"0d272d6a62d27498fe7f3fac94529cf41d7f405d","user":{"login":"vdauwera","id":2748435,"avatar_url":"https://avatars.githubusercontent.com/u/2748435?v=3","gravatar_id":"","url":"https://api.github.com/users/vdauwera","html_url":"https://github.com/vdauwera","followers_url":"https://api.github.com/users/vdauwera/followers","following_url":"https://api.github.com/users/vdauwera/following{/other_user}","gists_url":"https://api.github.com/users/vdauwera/gists{/gist_id}","starred_url":"https://api.github.com/users/vdauwera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vdauwera/subscriptions","organizations_url":"https://api.github.com/users/vdauwera/orgs","repos_url":"https://api.github.com/users/vdauwera/repos","events_url":"https://api.github.com/users/vdauwera/events{/privacy}","received_events_url":"https://api.github.com/users/vdauwera/received_events","type":"User","site_admin":false},"body":"\"The 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