{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/75046627","id":75046627,"diff_hunk":"@@ -0,0 +1,87 @@\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+\n+package picard.sam.markduplicates;\n+\n+import htsjdk.samtools.DuplicateSet;\n+import htsjdk.samtools.DuplicateSetIterator;\n+import htsjdk.samtools.SAMRecordDuplicateComparator;\n+import htsjdk.samtools.util.*;\n+import picard.cmdline.CommandLineProgramProperties;\n+import picard.cmdline.Option;\n+import picard.cmdline.programgroups.Alpha;\n+\n+/**\n+ * This is a simple tool to mark duplicates using the UmiAwareDuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.\n+ *\n+ * It makes use of the UmiAwareDuplicateSetIterator which is a wrapper around the DuplicateSetIterator.  It makes use\n+ * of the fact that duplicate sets with UMIs can be broken up into subsets based on information contained in the UMI.\n+ *\n+ * Users should continue to use MarkDuplicates in general, the main motivation for this tool is to provide a way to\n+ * mark duplicates using information from UMIs.\n+ *\n+ * @author fleharty\n+ */\n+@CommandLineProgramProperties(\n+        usage = \"Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. \" +\n+                \"All records are then written to the output file with the duplicate records flagged.\",\n+        usageShort = \"Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.\",\n+        programGroup = Alpha.class\n+)\n+\n+public class UmiAwareMarkDuplicatesWithMateCigar extends SimpleMarkDuplicatesWithMateCigar {\n+\n+    @Option(shortName = \"EDIT_DISTANCE_TO_JOIN\",\n+            doc = \"This option specifies the edit distance of UMIs to join\", optional = true)\n+    public int EDIT_DISTANCE_TO_JOIN = 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