gl-916 add pipeline version to metrics

src/main/java/picard/arrays/ArraysCallingMetricAccumulator.java

@@ -48,6 +48,7 @@ class ArraysCallingMetricAccumulator implements VariantProcessor.Accumulator<Arr
     private Integer p95Green;
     private Integer p95Red;
     private String scannerName;
+    private String pipelineVersion;
 
     /**
      * A map of sample names to metrics.  If .get() for a not-yet-existing sample name, a metric is generated, inserted into the map,
@@ -76,14 +77,15 @@ class ArraysCallingMetricAccumulator implements VariantProcessor.Accumulator<Arr
                         detail.P95_GREEN = p95Green;
                         detail.P95_RED = p95Red;
                         detail.SCANNER_NAME = scannerName;
+                        detail.PIPELINE_VERSION = pipelineVersion;
                         return detail;
                     }, true);
 
     ArraysCallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp) {
         this.dbsnp = dbsnp;
     }
 
-    public void setup(final VCFHeader vcfHeader) {
+    public void setup(final VCFHeader vcfHeader, final String pipelineVersion) {
         this.sampleAlias = InfiniumVcfFields.getValueFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.SAMPLE_ALIAS);
         this.analysisVersionNumber = InfiniumVcfFields.getOptionalIntegerFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.ANALYSIS_VERSION_NUMBER);
         this.chipTypeName = InfiniumVcfFields.getValueFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.ARRAY_TYPE);
@@ -103,6 +105,7 @@ public void setup(final VCFHeader vcfHeader) {
         this.p95Green = InfiniumVcfFields.getIntegerFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.P_95_GREEN);
         this.p95Red = InfiniumVcfFields.getIntegerFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.P_95_RED);
         this.scannerName = InfiniumVcfFields.getValueFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.SCANNER_NAME);
+        this.pipelineVersion = pipelineVersion;
 
         vcfHeader.getGenotypeSamples().forEach(sampleName -> sampleMetricsMap.get(sampleName));
     }

src/main/java/picard/arrays/CollectArraysVariantCallingMetrics.java

@@ -43,10 +43,14 @@ public class CollectArraysVariantCallingMetrics extends CommandLineProgram {
                     "<h4>Usage example:</h4>" +
                     "<pre>" +
                     "java -jar picard.jar CollectArraysVariantCallingMetrics \\<br />" +
+                    // TODO - ADD example
                     "      INPUT=genotyping_arrays.vcf \\<br />" +
                     "      OUTPUT=outputBaseName" +
                     "</pre>";
 
+    @Argument(doc = "The pipeline version used to create these metrics", optional = true)
+    public String PIPELINE_VERSION;
+
     @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input vcf file for analysis")
     public File INPUT;
 
@@ -106,7 +110,7 @@ protected int doWork() {
                 VariantProcessor.Builder
                         .generatingAccumulatorsBy(() -> {
                             ArraysCallingMetricAccumulator accumulator = new ArraysCallingMetricAccumulator(dbsnp);
-                            accumulator.setup(vcfHeader);
+                            accumulator.setup(vcfHeader, PIPELINE_VERSION);
                             return accumulator;
                         })
                         .combiningResultsBy(ArraysCallingMetricAccumulator.Result::merge)
@@ -438,6 +442,12 @@ public static class ArraysVariantCallingDetailMetrics extends CollectArraysVaria
         @MergeByAssertEquals
         public String SCANNER_NAME;
 
+        /**
+         * The version of the pipeline used for this sample
+         */
+        @MergeByAssertEquals
+        public String PIPELINE_VERSION;
+
         /**
          * Hidden fields not propagated to the metrics file.
          */

src/test/java/picard/arrays/CollectArraysVariantCallingMetricsTest.java

@@ -50,6 +50,7 @@ public void testCollectArraysVariantCallingMetricsOverkillTest(final String chip
 
         final CollectArraysVariantCallingMetrics collectArraysVariantCallingMetrics = new CollectArraysVariantCallingMetrics();
         collectArraysVariantCallingMetrics.INPUT = vcfFile;
+        collectArraysVariantCallingMetrics.PIPELINE_VERSION = "foo";
         collectArraysVariantCallingMetrics.DBSNP = dbSnpFile;
         collectArraysVariantCallingMetrics.OUTPUT = outputBaseFile;
         collectArraysVariantCallingMetrics.NUM_PROCESSORS = 1;
@@ -135,6 +136,7 @@ public void testCollectArraysVariantCallingMetricsOverkillTest(final String chip
             Assert.assertEquals(metrics.AUTOCALL_CALL_RATE, (float) metrics.NUM_AUTOCALL_CALLS / metrics.NUM_NON_FILTERED_ASSAYS, 0.0001);
 
             Assert.assertEquals(metrics.NUM_SINGLETONS, 7);
+            Assert.assertEquals(metrics.PIPELINE_VERSION, "foo");
         });
 
         Assert.assertEquals(detailMetrics.size(), 1, "Did not parse the desired number of detail metrics.");
@@ -243,6 +245,7 @@ public void testCollectArraysVariantCallingMetricsTwoSamples() throws IOExceptio
             Assert.assertEquals(metrics.AUTOCALL_CALL_RATE, (float) metrics.NUM_AUTOCALL_CALLS / metrics.NUM_NON_FILTERED_ASSAYS, 0.0001);
 
             Assert.assertEquals(metrics.NUM_SINGLETONS, 1);
+            Assert.assertNull(metrics.PIPELINE_VERSION);
         });
 
         Assert.assertEquals(detailMetrics.size(), 2, "Did not parse the desired number of detail metrics.");