{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/60473683","id":60473683,"diff_hunk":"@@ -58,20 +58,24 @@\n )\n public class ValidateSamFile extends CommandLineProgram {\n     static final String USAGE_SUMMARY = \"Validates a SAM or BAM file.  \";\n-    static final String USAGE_DETAILS = \"This tool reports on the validity of a SAM or BAM file relative to the SAM format specification \" +\n-            \"(see http://samtools.github.io/hts-specs/SAMv1.pdf), which is useful for troubleshooting errors encountered with other tools \" +\n-            \"that may be caused by improper formatting.<br /><br />\" +\n-            \"By default, the tool runs in VERBOSE mode and will exit after finding 100 errors and output them to the \" +\n-            \"console (stdout). It is often practical to start by running this tool with the SUMMARY mode option, which summarizes the \" +\n-            \"\\\"errors\\\" and \\\"warnings\\\". Consequently, specific validation warnings or errors that are of lesser concern can be ignored \" +\n-            \"using the IGNORE and/or IGNORE_WARNINGS arguments in order to focus on blocking errors. \" +\n-            \"<br />\" +\n+    static final String USAGE_DETAILS = \"<p>This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.  \" +\n+            \"For detailed information on the SAM specification, please see the SAM specification sheet <a href='http://samtools.github.io/hts-specs/SAMv1.pdf'>here</a>.</p> \" +\n+\n+            \"<p>Although the default setting for the tool runs in MODE=VERBOSE mode we highly recommend that you run the tool initially in MODE=SUMMARY.  \" +\n+            \"Running the tool in MODE=SUMMARY, will output a high-level overview including a list and a count of all 'WARNING' and/or 'ERROR' messages for your SAM/BAM file.  \" +\n+            \"Subsequently running the tool in MODE=VERBOSE will output a detailed list of every record with a 'WARNING' and/or 'ERROR' message.\"+\n+            \"  Validation errors or warnings that are of lesser concern can be ignored using the IGNORE and/or IGNORE_WARNINGS arguments \" +\n+            \"to prioritize blocking errors.</p> \" +\n+            \"<p>After identifying and fixing your 'warnings/errors', we recommend that you rerun this tool to validate your SAM/BAM file prior to\" +\n+            \" inputting directly into <a href='http://broadinstitute.github.io/picard/'>Picard</a> or <a href='https://www.broadinstitute.org/gatk/'>GATK</a>.</p>\" +\n             \"<h4>Usage example:</h4>\" +\n             \"<pre>\" +\n             \"java -jar picard.jar ValidateSamFile \\\\<br />\" +\n-            \"     I=input.bam \\\\<br />\" +\n-            \"     MODE=SUMMARY\" +\n+            \"      I=input.bam \\\\<br />\" +\n+            \"      MODE=SUMMARY\" +\n             \"</pre>\" +\n+            \"\" +\n+            \"<p>To obtain a complete list with descriptions of both 'ERROR' and 'WARNING' messages, please visit the <a href='http://gatkforums.broadinstitute.org/gatk/discussion/6956'>Common Problems</a> forum link.\"+","path":"src/java/picard/sam/ValidateSamFile.java","position":31,"original_position":31,"commit_id":"a4aae9de64a0d38ba99ee9318a4dabd6e2350e8c","original_commit_id":"a4aae9de64a0d38ba99ee9318a4dabd6e2350e8c","user":{"login":"dekling","id":8260472,"avatar_url":"https://avatars.githubusercontent.com/u/8260472?v=3","gravatar_id":"","url":"https://api.github.com/users/dekling","html_url":"https://github.com/dekling","followers_url":"https://api.github.com/users/dekling/followers","following_url":"https://api.github.com/users/dekling/following{/other_user}","gists_url":"https://api.github.com/users/dekling/gists{/gist_id}","starred_url":"https://api.github.com/users/dekling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dekling/subscriptions","organizations_url":"https://api.github.com/users/dekling/orgs","repos_url":"https://api.github.com/users/dekling/repos","events_url":"https://api.github.com/users/dekling/events{/privacy}","received_events_url":"https://api.github.com/users/dekling/received_events","type":"User","site_admin":false},"body":"Will do.","created_at":"2016-04-20T19:37:41Z","updated_at":"2016-04-20T19:37:41Z","html_url":"https://github.com/broadinstitute/picard/pull/521#discussion_r60473683","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/521","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/60473683"},"html":{"href":"https://github.com/broadinstitute/picard/pull/521#discussion_r60473683"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/521"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/521","id":67178482,"html_url":"https://github.com/broadinstitute/picard/pull/521","diff_url":"https://github.com/broadinstitute/picard/pull/521.diff","patch_url":"https://github.com/broadinstitute/picard/pull/521.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/521","number":521,"state":"open","locked":false,"title":"Adjusted text for 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