{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/38987220","id":38987220,"diff_hunk":"@@ -47,17 +47,30 @@\n  * @author ktibbett@broadinstitute.org\n  */\n @CommandLineProgramProperties(\n-        usage = \"Merges alignment data from a SAM or BAM \" +\n-                \"file with additional data stored in an unmapped BAM file and produces a third SAM \" +\n-                \"or BAM file of aligned and unaligned reads. The purpose is to use information from the \" +\n-                \"unmapped BAM to fix up aligner output, so that the resulting file is valid for use by other \" +\n-                \"Picard programs. For simple BAM file merges, use MergeSamFiles. NOTE that MergeBamAlignment expects to \" +\n-                \"find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it \" +\n-                \"to have the same base name as the reference fasta except with the extension '.dict'\",\n-        usageShort = \"Merges alignment data from a SAM or BAM with data in an unmapped BAM file\",\n+        usage = MergeBamAlignment.USAGE_SUMMARY + MergeBamAlignment.USAGE_DETAILS,\n+        usageShort = MergeBamAlignment.USAGE_SUMMARY,\n         programGroup = SamOrBam.class\n )\n public class MergeBamAlignment extends CommandLineProgram {\n+    static final String USAGE_SUMMARY = \"Merges alignment data from a SAM or BAM with data in an unmapped BAM file.  \";\n+    static final String USAGE_DETAILS = \"Produces a third SAM or BAM file with additional data stored in an\" +\n+            \" unmapped BAM file in addition to the aligned and unaligned reads.  The purpose of this tool\" +\n+            \" is to use information from the unmapped BAM to fix up aligner output.  The resulting file will be valid \" +\n+            \"for use by other Picard tools.  For simple BAM file merges, use MergeSamFiles.  NOTE that MergeBamAlignment expects to \" +\n+            \"find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it \" +\n+            \"to have the same base name as the reference fasta except with the extension \\\".dict\\\". \"         +\n+            \"<h4>Usage example:</h4>\" +\n+            \"<pre>\" +\n+            \"java -jar picard.jar MergeBamAlignment \\\\<br /> \" +\n+            \"      UNMAPPED=umBAM.bam \\\\ <br /> \" +\n+            \"      O=merge_BAM_alignment.bam \\\\<br /> \" +","path":"src/java/picard/sam/MergeBamAlignment.java","position":28,"original_position":28,"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":"ALIGNED_BAM should be specified as part of this example (it's where the alignment data that's being merged in comes from).","created_at":"2015-09-08T22:15:54Z","updated_at":"2015-09-08T22:15:54Z","html_url":"https://github.com/broadinstitute/picard/pull/230#discussion_r38987220","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/230","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/38987220"},"html":{"href":"https://github.com/broadinstitute/picard/pull/230#discussion_r38987220"},"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 tools","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":"Added usage examples and provided detailed explanations for 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