{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/79312948","id":79312948,"diff_hunk":"@@ -0,0 +1,113 @@\n+/*\n+ * The MIT License\n+ *\n+ * Copyright (c) 2016 The Broad Institute\n+ *\n+ * Permission is hereby granted, free of charge, to any person obtaining a copy\n+ * of this software and associated documentation files (the \"Software\"), to deal\n+ * in the Software without restriction, including without limitation the rights\n+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n+ * copies of the Software, and to permit persons to whom the Software is\n+ * furnished to do so, subject to the following conditions:\n+ *\n+ * The above copyright notice and this permission notice shall be included in\n+ * all copies or substantial portions of the Software.\n+ *\n+ * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n+ * THE SOFTWARE.\n+ */\n+package picard.sam;\n+\n+import htsjdk.samtools.SAMException;\n+import htsjdk.samtools.SAMFileHeader;\n+import htsjdk.samtools.SAMFileWriter;\n+import htsjdk.samtools.SAMFileWriterFactory;\n+import htsjdk.samtools.SamReader;\n+import htsjdk.samtools.SamReaderFactory;\n+import htsjdk.samtools.reference.ReferenceSequenceFileWalker;\n+import htsjdk.samtools.util.CloserUtil;\n+import htsjdk.samtools.util.IOUtil;\n+import htsjdk.samtools.util.Log;\n+import htsjdk.samtools.util.ProgressLogger;\n+import picard.cmdline.CommandLineProgram;\n+import picard.cmdline.CommandLineProgramProperties;\n+import picard.cmdline.Option;\n+import picard.cmdline.StandardOptionDefinitions;\n+import picard.cmdline.programgroups.SamOrBam;\n+\n+import java.io.File;\n+import java.util.stream.StreamSupport;\n+\n+/**\n+ * @author Yossi Farjoun\n+ */\n+@CommandLineProgramProperties(\n+        usage = SetNmMdAndUqTags.USAGE_SUMMARY + SetNmMdAndUqTags.USAGE_DETAILS,\n+        usageShort = SetNmMdAndUqTags.USAGE_SUMMARY,\n+        programGroup = SamOrBam.class\n+)\n+public class SetNmMdAndUqTags extends CommandLineProgram {\n+    static final String USAGE_SUMMARY = \"Fixes the NM, MD, and UQ tags in a SAM file.  \";\n+    static final String USAGE_DETAILS = \"This tool takes in a SAM or BAM file (sorted by coordinate) and calculates the NM, MD, and UQ tags by comparing with the reference.\"+\n+            \"<br />\" +\n+                    \"This may be needed when MergeBamAlignment was run with SORT_ORDER different from 'coordinate' and thus could not fix\\n\"+\n+                    \"these tags then.<br />\"+\n+            \"<h4>Usage example:</h4>\" +\n+            \"<pre>\" +\n+            \"java -jar picard.jar SetNmMDAndUqTags \\\\<br />\" +\n+            \"      I=sorted.bam \\\\<br />\" +\n+            \"      O=fixed.bam \\\\<br />\"+\n+            \"</pre>\" +\n+            \"<hr />\";\n+    @Option(doc = \"The BAM or SAM file to fix.\", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME)\n+    public File INPUT;\n+\n+    @Option(doc = \"The fixed BAM or SAM output file. \", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME)\n+    public File OUTPUT;\n+\n+    @Option(doc = \"Whether the file contains bisulfite sequence (used when calculating the NM tag).\")\n+    public boolean IS_BISULFITE_SEQUENCE = false;\n+\n+    @Override\n+    protected String[] customCommandLineValidation() {\n+        if (REFERENCE_SEQUENCE == null) {\n+            return new String[]{\"Must have a non-null REFERENCE_SEQUENCE\"};\n+        }\n+        return super.customCommandLineValidation();\n+    }\n+\n+    private final Log log = Log.getInstance(SetNmMdAndUqTags.class);\n+\n+    public static void main(final String[] argv) {\n+        new SetNmMdAndUqTags().instanceMainWithExit(argv);\n+    }\n+\n+    protected int doWork() {\n+        IOUtil.assertFileIsReadable(INPUT);\n+        IOUtil.assertFileIsWritable(OUTPUT);\n+        final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);\n+\n+        if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {\n+            throw new SAMException(\"Input must be coordinate-sorted for this program to run. Found: \" + reader.getFileHeader().getSortOrder());\n+        }\n+\n+        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);\n+        writer.setProgressLogger(\n+                new ProgressLogger(log, (int) 1e7, \"Wrote\", \"records\"));\n+\n+        final ReferenceSequenceFileWalker refSeq = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);\n+\n+       StreamSupport.stream(reader.spliterator(),false)","path":"src/main/java/picard/sam/SetNmMdAndUqTags.java","position":105,"original_position":105,"commit_id":"57c0ac1338614197633df36b75c7a9a86b5c0f72","original_commit_id":"57c0ac1338614197633df36b75c7a9a86b5c0f72","user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"body":"extra space missing here?","created_at":"2016-09-18T19:10:22Z","updated_at":"2016-09-18T19:10:56Z","html_url":"https://github.com/broadinstitute/picard/pull/636#discussion_r79312948","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/636","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/79312948"},"html":{"href":"https://github.com/broadinstitute/picard/pull/636#discussion_r79312948"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/636"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/636","id":82065420,"html_url":"https://github.com/broadinstitute/picard/pull/636","diff_url":"https://github.com/broadinstitute/picard/pull/636.diff","patch_url":"https://github.com/broadinstitute/picard/pull/636.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/636","number":636,"state":"open","locked":false,"title":"Rename SetNmAndUqTags and fix #622 (MergeBamAlignment MD tag).","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"body":"@yfarjoun @tfenne \r\n\r\n1. Rename SetNmAndUqTags to SetNmMDAndUqTags.\r\nWIP\r\n2. Fixes: https://github.com/broadinstitute/picard/pull/622\r\n\r\nFixes https://github.com/broadinstitute/picard/issues/634 as an alternate to reverting 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