GSA-491: Add hidden tag to GATK that propagates to the GATK logs

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -64,12 +64,35 @@ public class GATKArgumentCollection {
     @Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false)
     public Integer readBufferSize = null;
 
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // GATKRunReport options
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
     @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
     public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
 
     @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
     public File gatkKeyFile = null;
 
+    /**
+     * The GATKRunReport supports (as of GATK 2.2) tagging GATK runs with an arbitrary String tag that can be
+     * used to group together runs during later analysis.  One use of this capability is to tag runs as GATK
+     * performance tests, so that the performance of the GATK over time can be assessed from the logs directly.
+     *
+     * Note that the tags do not conform to any ontology, so you are free to use any tags that you might find
+     * meaningful.
+     */
+    @Argument(fullName = "tag", shortName = "tag", doc="Arbitrary tag string to identify this GATK run as part of a group of runs, for later analysis", required = false)
+    public String tag = "NA";
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // XXX
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
     @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
     public List<String> readFilters = new ArrayList<String>();
 

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -138,6 +138,9 @@ public class GATKRunReport {
     @Element(required = true, name = "iterations")
     private long nIterations;
 
+    @Element(required = true, name = "tag")
+    private String tag;
+
     public enum PhoneHomeOption {
         /** Disable phone home */
         NO_ET,
@@ -186,6 +189,8 @@ public class GATKRunReport {
             nIterations = engine.getCumulativeMetrics().getNumIterations();
         }
 
+        tag = engine.getArguments().tag;
+
         // user and hostname -- information about the runner of the GATK
         userName = System.getProperty("user.name");
         hostName = Utils.resolveHostname();