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,
@@ -76,6 +77,7 @@ 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);
 
@@ -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 = InfiniumVcfFields.getOptionalValueFromVcfOtherHeaderLine(vcfHeader, InfiniumVcfFields.PIPELINE_VERSION);
 
         vcfHeader.getGenotypeSamples().forEach(sampleName -> sampleMetricsMap.get(sampleName));
     }

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

@@ -43,10 +43,12 @@ 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(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input vcf file for analysis")
     public File INPUT;
 
@@ -438,6 +440,12 @@ 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/main/java/picard/arrays/GtcToVcf.java

@@ -140,6 +140,9 @@ public class GtcToVcf extends CommandLineProgram {
     @Argument(doc = "The sample alias")
     public String SAMPLE_ALIAS;
 
+    @Argument(doc = "The version of the pipeline used to generate this VCF", optional = true)
+    public String PIPELINE_VERSION;
+
     @Argument(doc = "The analysis version of the data used to generate this VCF", optional = true)
     public Integer ANALYSIS_VERSION_NUMBER;
 
@@ -538,6 +541,9 @@ private VCFHeader createVCFHeader(final Build37ExtendedIlluminaManifest manifest
         if (EXPECTED_GENDER != null) {
             lines.add(new VCFHeaderLine(InfiniumVcfFields.EXPECTED_GENDER, EXPECTED_GENDER));
         }
+        if (PIPELINE_VERSION != null) {
+            lines.add(new VCFHeaderLine(InfiniumVcfFields.PIPELINE_VERSION, PIPELINE_VERSION.toString()));
+        }
         //add control codes
         final int measurementCount = gtcFile.getRawControlXIntensities().length / ArraysControlInfo.CONTROL_INFO.length;
         for (int i = 0; i < ArraysControlInfo.CONTROL_INFO.length; i++) {

src/main/java/picard/arrays/illumina/InfiniumVcfFields.java

@@ -57,6 +57,7 @@ public class InfiniumVcfFields {
     public static final String P_95_RED = "p95Red";
     public static final String P_95_GREEN = "p95Green";
     public static final String SCANNER_NAME = "scannerName";
+    public static final String PIPELINE_VERSION = "pipelineVersion";
 
     //FORMAT Fields
     public static final String X = "X";

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

@@ -135,6 +135,7 @@ 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 +244,7 @@ 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.");

testdata/picard/arrays/7991775143_R01C01.vcf

@@ -185,6 +185,7 @@
 ##p95Green=4251
 ##p95Red=5479
 ##picardVersion=Version:054660cc27c208419607db4f10ba598284dd545f
+##pipelineVersion=foo
 ##reference=/cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta
 ##sampleAlias=NA12878
 ##scannerName=N370

testdata/picard/arrays/7991775143_R01C01_wo_optional_fields.vcf

@@ -179,6 +179,7 @@
 ##p95Green=4251
 ##p95Red=5479
 ##picardVersion=2.20.3-17-g8331bf3-SNAPSHOT
+##pipelineVersion=foo
 ##reference=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
 ##sampleAlias=NA12878
 ##scannerName=N370