.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="src/java"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="lib/testng/testng-5.5-jdk15.jar"/>
- <classpathentry kind="lib" path="lib/ant/bcel-5.2.jar"/>
- <classpathentry kind="output" path="bin"/>
-</classpath>

.project

-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>picard</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
-</projectDescription>

Dockerfile

 FROM broadinstitute/java-baseimage
 MAINTAINER Broad Institute DSDE <dsde-engineering@broadinstitute.org>
 
+ARG build_command=shadowJar
+ARG jar_name=picard.jar
+
 # Install ant, git for building
 RUN apt-get update && \
     apt-get --no-install-recommends install -y --force-yes \
         git \
+        r-base \
         ant && \
     apt-get clean autoclean && \
     apt-get autoremove -y
@@ -14,8 +18,8 @@ COPY / /usr/picard/
 WORKDIR /usr/picard
 
 # Build the distribution jar, clean up everything else
-RUN ./gradlew shadowJar && \
-    mv build/libs/picard.jar picard.jar && \
+RUN ./gradlew ${build_command} && \
+    mv build/libs/${jar_name} picard.jar && \
     mv src/main/resources/picard/docker_helper.sh docker_helper.sh && \
     ./gradlew clean && \
     rm -rf src && \

build.gradle

@@ -47,7 +47,24 @@ jacoco {
     toolVersion = "0.7.5.201505241946"
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '2.14.3')
+final requiredJavaVersion = "8"
+final buildPrerequisitesMessage = "See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard"
+// Ensure that we have the right JDK version, a clone of the git repository
+def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) {
+    // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
+    if (ToolProvider.getSystemToolClassLoader() == null) {
+        throw new GradleException(
+                "The ClassLoader obtained from the Java ToolProvider is null. "
+                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
+    }
+    if (!file(".git").isDirectory()) {
+        throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "
+                + "$buildPrerequisitesMessage")
+    }
+}
+ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage)
+
+final htsjdkVersion = System.getProperty('htsjdk.version', '2.16.1')
 
 // We use a custom shaded build of the NIO library to avoid a regression in the authentication layer.
 // GATK does the same, see https://github.com/broadinstitute/gatk/issues/3591
@@ -68,10 +85,11 @@ configurations {
 }
 
 dependencies {
-    compile('com.intel.gkl:gkl:0.8.2') {
+    compile('com.intel.gkl:gkl:0.8.5') {
         exclude module: 'htsjdk'
     }
     compile 'com.google.guava:guava:15.0'
+    compile 'org.apache.commons:commons-math3:3.5'
     compile 'com.github.samtools:htsjdk:' + htsjdkVersion
     compile 'org.broadinstitute:barclay:2.0.0'
     compileOnly googleNio

build_push_docker.sh

+#!/usr/bin/env bash
+
+# This script is used to build and deploy docker images for Picard
+
+if [[ "$1" == "" ]]
+then
+    echo "Usage: build_push_docker.sh <git-tag>"
+    exit 1
+fi
+
+declare -r TAG=${1}
+
+declare -r PICARD_TAG=broadinstitute/picard:${TAG}
+declare -r PICARD_CLOUD_TAG=us.gcr.io/broad-gotc-prod/picard-cloud:${TAG}
+
+echo "Will build and push the following docker images:"
+echo ${PICARD_TAG}
+echo ${PICARD_CLOUD_TAG}
+
+read -p "Is this really what you want to do? " -n 1 -r
+echo    # (optional) move to a new line
+if [[ $REPLY =~ ^[Yy]$ ]]
+then
+    docker build -t ${PICARD_TAG} --build-arg build_command=shadowJar --build-arg jar_name=picard.jar .
+    docker build -t ${PICARD_CLOUD_TAG} --build-arg build_command=cloudJar --build-arg jar_name=picardcloud.jar .
+
+    docker push ${PICARD_TAG}
+    gcloud docker -- push ${PICARD_CLOUD_TAG}
+fi

debian/changelog

+picard-tools (2.18.14+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.2.1
+  * Fix link
+    Closes: #905706
+
+ -- Andreas Tille <tille@debian.org>  Mon, 17 Sep 2018 15:13:19 +0200
+
 picard-tools (2.18.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -27,7 +27,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
                libhtsjdk-java-doc,
                libguava-java-doc,
                libjs-jquery
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/picard-tools
 Vcs-Git: https://salsa.debian.org/med-team/picard-tools.git
 Homepage: http://broadinstitute.github.io/picard/

debian/libpicard-java-doc.links

-usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js usr/share/javascript/jquery/jquery.min.js
+usr/share/javascript/jquery/jquery.min.js	usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js

debian/patches/10-build.xml.patch

@@ -4,7 +4,7 @@ Forwarded: not-needed
 Last-Updated: 2016-07-07
 --- a/build.gradle
 +++ b/build.gradle
-@@ -12,13 +12,7 @@
+@@ -12,13 +12,7 @@ plugins {
      id "java"
      id 'maven'
      id 'signing'
@@ -18,7 +18,7 @@ Last-Updated: 2016-07-07
  }
  
  mainClassName = "picard.cmdline.PicardCommandLine"
-@@ -31,6 +25,7 @@
+@@ -31,6 +25,7 @@ repositories {
      }
  }
  
@@ -26,15 +26,15 @@ Last-Updated: 2016-07-07
  jacocoTestReport {
      dependsOn test
      group = "Reporting"
-@@ -46,6 +41,7 @@
+@@ -46,6 +41,7 @@ jacocoTestReport {
  jacoco {
      toolVersion = "0.7.5.201505241946"
  }
 +*/
  
- final htsjdkVersion = System.getProperty('htsjdk.version', '2.14.3')
- 
-@@ -56,7 +52,7 @@
+ final requiredJavaVersion = "8"
+ final buildPrerequisitesMessage = "See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard"
+@@ -73,7 +69,7 @@ final googleNio = 'org.broadinstitute:go
  // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
  // test execution, and gatkDoc generation, but we don't want them as part of the runtime
  // classpath and we don't want to redistribute them in the uber jar.
@@ -43,13 +43,7 @@ Last-Updated: 2016-07-07
  
  configurations {
      cloudConfiguration {
-@@ -72,13 +68,14 @@
-         exclude module: 'htsjdk'
-     }
-     compile 'com.google.guava:guava:15.0'
-+    compile 'org.broadinstitute:gatk-native-bindings:debian'
-     compile 'com.github.samtools:htsjdk:' + htsjdkVersion
-     compile 'org.broadinstitute:barclay:2.0.0'
+@@ -95,8 +91,8 @@ dependencies {
      compileOnly googleNio
  
      // javadoc utilities; compile/test only to prevent redistribution of sdk jars
@@ -60,7 +54,7 @@ Last-Updated: 2016-07-07
  
      testCompile 'org.testng:testng:6.9.10'
      testCompile 'org.apache.commons:commons-lang3:3.6'
-@@ -94,9 +91,18 @@
+@@ -112,9 +108,18 @@ configurations.all {
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -81,7 +75,7 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -148,6 +154,8 @@
+@@ -166,6 +171,8 @@ jar {
  tasks.withType(Javadoc) {
      // do this for all javadoc tasks, including gatkDoc
      options.addStringOption('Xdoclint:none')
@@ -90,7 +84,7 @@ Last-Updated: 2016-07-07
  }
  
  javadoc {
-@@ -174,7 +182,8 @@
+@@ -192,7 +199,8 @@ task picardDoc(type: Javadoc, dependsOn:
  
      // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
      // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
@@ -100,7 +94,7 @@ Last-Updated: 2016-07-07
      options.docletpath = classpath.asType(List)
      options.doclet = "picard.util.help.PicardHelpDoclet"
  
-@@ -261,6 +270,8 @@
+@@ -279,6 +287,8 @@ tasks.withType(Test) {
          }
      }
  
@@ -109,7 +103,7 @@ Last-Updated: 2016-07-07
      // set heap size for the test JVM(s)
      minHeapSize = "1G"
      maxHeapSize = "2G"
-@@ -397,6 +408,7 @@
+@@ -415,6 +425,7 @@ task copyPicardDoc(dependsOn: 'picardDoc
      into "$htmlDir/picarddoc"
  }
  
@@ -117,7 +111,7 @@ Last-Updated: 2016-07-07
  task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){
    outputs.dir htmlDir
  }
-@@ -412,3 +424,4 @@
+@@ -430,3 +441,4 @@ githubPages {
      into 'newdocs'
    }
  }

debian/patches/20-shadowjar.patch

@@ -2,7 +2,7 @@ Description: do not use shadowjar
 Author: Sascha Steinbiss <satta@debian.org>
 --- a/build.gradle
 +++ b/build.gradle
-@@ -109,7 +109,7 @@
+@@ -126,7 +126,7 @@ group = 'com.github.broadinstitute'
  
  defaultTasks 'all'
  
@@ -11,7 +11,7 @@ Author: Sascha Steinbiss <satta@debian.org>
  
  // Source file names for the picard command line properties file. We select and include only one of
  // these two files in each jar, renamed to "picardCmdLine.properties", depending on which parser we
-@@ -197,6 +197,7 @@
+@@ -214,6 +214,7 @@ task picardDoc(type: Javadoc, dependsOn:
      options.addStringOption("verbose")
  }
  
@@ -19,7 +19,7 @@ Author: Sascha Steinbiss <satta@debian.org>
  task currentJar(type: Copy){
      from shadowJar
      into new File(buildDir, "libs")
-@@ -214,8 +215,7 @@
+@@ -231,8 +232,7 @@ shadowJar {
          }
      }
  }

debian/patches/40-tests-fix-testng.patch

@@ -4,7 +4,7 @@ Description: Fix testng version
 
 --- a/build.gradle
 +++ b/build.gradle
-@@ -57,9 +57,6 @@
+@@ -74,9 +74,6 @@ final googleNio = 'org.broadinstitute:go
  configurations {
      cloudConfiguration {
          extendsFrom runtime
@@ -14,8 +14,8 @@ Description: Fix testng version
      }
  }
  
-@@ -71,14 +68,13 @@
-     compile 'org.broadinstitute:gatk-native-bindings:debian'
+@@ -88,14 +85,13 @@ dependencies {
+     compile 'org.apache.commons:commons-math3:3.5'
      compile 'com.github.samtools:htsjdk:' + htsjdkVersion
      compile 'org.broadinstitute:barclay:2.0.0'
 -    compileOnly googleNio
@@ -31,7 +31,7 @@ Description: Fix testng version
  }
  
  configurations.all {
-@@ -217,6 +213,7 @@
+@@ -234,6 +230,7 @@ shadowJar {
  }
  */
  
@@ -39,7 +39,7 @@ Description: Fix testng version
  task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar)  {
      configurations = [project.configurations.cloudConfiguration]
      from project.sourceSets.main.output
-@@ -241,6 +238,7 @@
+@@ -258,6 +255,7 @@ task barclayShadowJar(type: com.github.j
      }
      archiveName 'picardBarclay.jar'
  }
@@ -47,7 +47,7 @@ Description: Fix testng version
  
  // Run the tests using the legacy parser only. Assumes that test code is written using
  // legacy command line parser syntax.
-@@ -251,6 +249,8 @@
+@@ -268,6 +266,8 @@ task legacyTest(type: Test)
  task barclayTest(type: Test) {
      systemProperty 'picard.convertCommandLine', 'true'
      systemProperty 'picard.useLegacyParser', 'false'
@@ -56,7 +56,7 @@ Description: Fix testng version
  }
  
  // Run tests using both the legacy and barclay command line parsers.
-@@ -262,6 +262,9 @@
+@@ -279,6 +279,9 @@ tasks.withType(Test) {
      outputs.upToDateWhen { false } // tests will always rerun
      description = "Runs the unit tests"
  
@@ -68,7 +68,7 @@ Description: Fix testng version
              excludeGroups "slow", "broken"
 --- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
 +++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
-@@ -41,51 +41,6 @@
+@@ -41,51 +41,6 @@ public class CollectHsMetricsTest extend
          };
      }
  
@@ -120,7 +120,7 @@ Description: Fix testng version
  
      @Test
      public void testCoverageHistogram() throws IOException {
-@@ -106,7 +61,7 @@
+@@ -106,7 +61,7 @@ public class CollectHsMetricsTest extend
          final boolean clipOverlappingReads = true;
          final int sampleSize = 10;
  
@@ -131,7 +131,7 @@ Description: Fix testng version
          final String[] args = new String[] {
 --- a/src/test/java/picard/analysis/artifacts/TransitionTest.java
 +++ b/src/test/java/picard/analysis/artifacts/TransitionTest.java
-@@ -34,13 +34,4 @@
+@@ -34,13 +34,4 @@ public class TransitionTest {
          return new Object[][] {{Character.MIN_VALUE}, {Transition.Base.A.base - 1}, {'Z'}, {Character.MAX_VALUE}};
      }
  
@@ -147,7 +147,7 @@ Description: Fix testng version
  }
 --- a/src/test/java/picard/util/IntervalListToolsTest.java
 +++ b/src/test/java/picard/util/IntervalListToolsTest.java
-@@ -80,12 +80,6 @@
+@@ -80,12 +80,6 @@ public class IntervalListToolsTest exten
          };
      }
  

debian/patches/fix_javadoc_ascii.patch

---- a/src/main/java/picard/util/LiftoverUtils.java
-+++ b/src/main/java/picard/util/LiftoverUtils.java
-@@ -324,7 +324,7 @@
-      *    Note: this will modify the start/stop and alleles of this builder.
-      *    Also note: if the reference allele does not match the reference sequence, this method will throw an exception
-      *
--     *    Based on Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015)
-+     *    Based on Adrian Tan, G. R. Abecasis and Hyun Min Kang. (2015)
-      *    Unified Representation of Genetic Variants. Bioinformatics.
-      *
-      */
+Author: Olivier Sallou
+Last-Update: 2018-04-23 14:51:06 +0000
+Description: Fix some issues with JavaDoc
+
 --- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
 +++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
 @@ -23,7 +23,6 @@

debian/patches/fix_test_freezing

-Subject: unit test freezing
-Description: this patch should prevent test to remain running after error,
- applied upstream in master:
- https://github.com/broadinstitute/picard/commit/4c2e22a9c591b8b7e8a427d33478e43d45c113b5
---- a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java
-+++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java
-@@ -152,7 +152,7 @@
-         completedWorkExecutor.shutdown();
- 
-         //thread by surface tile
--        final ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads);
-+        final ThreadPoolExecutorWithExceptions tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads);
- 
-         for (final Integer tile : tiles) {
-             tileProcessingExecutor.submit(new TileProcessor(tile, barcodesFiles.get(tile)));
-@@ -161,10 +161,18 @@
-         tileProcessingExecutor.shutdown();
- 
-         awaitThreadPoolTermination("Reading executor", tileProcessingExecutor);
--        awaitThreadPoolTermination("Tile completion executor", completedWorkExecutor);
- 
--        barcodeWriterThreads.values().forEach(ThreadPoolExecutor::shutdown);
--        barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor));
-+        // if there was an exception reading then initiate an immediate shutdown.
-+        if (tileProcessingExecutor.exception != null) {
-+            int tasksStillRunning = completedWorkExecutor.shutdownNow().size();
-+            tasksStillRunning += barcodeWriterThreads.values().stream().mapToLong(executor -> executor.shutdownNow().size()).sum();
-+            throw new PicardException("Reading executor had exceptions. There were " + tasksStillRunning
-+                    + " tasks were still running or queued and have been cancelled.", tileProcessingExecutor.exception);
-+        } else {
-+            awaitThreadPoolTermination("Tile completion executor", completedWorkExecutor);
-+            barcodeWriterThreads.values().forEach(ThreadPoolExecutor::shutdown);
-+            barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor));
-+        }
-     }
- 
-     private void awaitThreadPoolTermination(final String executorName, final ThreadPoolExecutor executorService) {
-@@ -175,7 +183,7 @@
-                         executorService.getQueue().size()));
-             }
-         } catch (final InterruptedException e) {
--            e.printStackTrace();
-+            log.error("Interrupted exception caught: ", e);
-         }
-     }
- 
-@@ -278,12 +286,12 @@
-             final int maxRecordsInRam =
-                     Math.max(1, maxReadsInRamPerTile /
-                             barcodeRecordWriterMap.size());
--            return SortingCollection.newInstance(
-+            return SortingCollection.newInstanceFromPaths(
-                     outputRecordClass,
-                     codecPrototype.clone(),
-                     outputRecordComparator,
-                     maxRecordsInRam,
--                    tmpDirs);
-+                    IOUtil.filesToPaths(tmpDirs));
-         }
-     }
- 
---- a/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java
-+++ b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java
-@@ -14,6 +14,7 @@
-  * while executing
-  */
- public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor {
-+    public Throwable exception = null;
-     /**
-      * Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.
-      *
-@@ -40,6 +41,7 @@
-             }
-         }
-         if (t != null) {
-+            exception = t;
-             throw new PicardException(t.getMessage(), t);
-         }
-     }

debian/patches/series

@@ -4,4 +4,3 @@
 40-tests-fix-testng.patch
 remove_google_nio.patch
 fix_javadoc_ascii.patch
-fix_test_freezing

project/plugins.sbt

-addSbtPlugin("de.johoop" % "sbt-testng-plugin" % "3.0.2")
-
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.13.0")
-
-addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "0.7.1")
\ No newline at end of file

src/main/java/picard/analysis/AbstractWgsMetricsCollector.java

@@ -184,8 +184,7 @@ public abstract class AbstractWgsMetricsCollector<T extends AbstractRecordAndOff
                 basesExcludedByCapping,
                 coverageCap,
                 getUnfilteredBaseQHistogram(),
-                collectWgsMetrics.SAMPLE_SIZE
-        );
+                collectWgsMetrics.SAMPLE_SIZE);
     }
 
     /**

src/main/java/picard/analysis/AlignmentSummaryMetrics.java

@@ -131,7 +131,7 @@ public class AlignmentSummaryMetrics extends MultilevelMetrics {
     public long READS_ALIGNED_IN_PAIRS;
 
     /**
-     * The fraction of reads whose mate pair was also aligned to the reference.
+     * The fraction of aligned reads whose mate pair was also aligned to the reference.
      * READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED
      */
     public double PCT_READS_ALIGNED_IN_PAIRS;

src/main/java/picard/analysis/CollectWgsMetrics.java

@@ -49,9 +49,7 @@ import picard.filter.CountingPairedFilter;
 import picard.util.MathUtil;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
 
 import static picard.cmdline.StandardOptionDefinitions.MINIMUM_MAPPING_QUALITY_SHORT_NAME;
 
@@ -122,6 +120,12 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
     @ArgumentCollection
     protected IntervalArgumentCollection intervalArugmentCollection = makeIntervalArgumentCollection();
 
+    @Argument(doc="Output for Theoretical Sensitivity metrics.", optional = true)
+    public File THEORETICAL_SENSITIVITY_OUTPUT;
+
+    @Argument(doc="Allele fraction for which to calculate theoretical sensitivity.", optional = true)
+    public List<Double> ALLELE_FRACTION = new ArrayList<>(Arrays.asList(0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5));
+
     @Argument(doc = "If true, fast algorithm is used.")
     public boolean USE_FAST_ALGORITHM = false;
 
@@ -155,7 +159,7 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
                 optional = true)
         public File INTERVALS;
 
-        public File getIntervalFile() { return INTERVALS; };
+        public File getIntervalFile() { return INTERVALS; }
     };
 
     /** Metrics for evaluating the performance of whole genome sequencing experiments. */
@@ -434,10 +438,6 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
         }
     }
 
-    public static void main(final String[] args) {
-        new CollectWgsMetrics().instanceMainWithExit(args);
-    }
-
     /** Gets the SamReader from which records will be examined.  This will also set the header so that it is available in
      *  */
     protected SamReader getSamReader() {
@@ -455,6 +455,9 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
         if (INTERVALS != null) {
             IOUtil.assertFileIsReadable(INTERVALS);
         }
+        if (THEORETICAL_SENSITIVITY_OUTPUT != null) {
+            IOUtil.assertFileIsWritable(THEORETICAL_SENSITIVITY_OUTPUT);
+        }
 
         // it doesn't make sense for the locus accumulation cap to be lower than the coverage cap
         if (LOCUS_ACCUMULATION_CAP < COVERAGE_CAP) {
@@ -483,7 +486,7 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
         iterator.setMappingQualityScoreCutoff(0); // Handled separately because we want to count bases
         iterator.setIncludeNonPfReads(false);
 
-        final AbstractWgsMetricsCollector collector = getCollector(COVERAGE_CAP, getIntervalsToExamine());
+        final AbstractWgsMetricsCollector<?> collector = getCollector(COVERAGE_CAP, getIntervalsToExamine());
         final WgsMetricsProcessor processor = getWgsMetricsProcessor(progress, refWalker, iterator, collector);
         processor.processFile();
 
@@ -491,6 +494,15 @@ static final String USAGE_DETAILS = "<p>This tool collects metrics about the fra
         processor.addToMetricsFile(out, INCLUDE_BQ_HISTOGRAM, dupeFilter, mapqFilter, pairFilter);
         out.write(OUTPUT);
 
+        if (THEORETICAL_SENSITIVITY_OUTPUT != null) {
+            // Write out theoretical sensitivity results.
+            final MetricsFile<TheoreticalSensitivityMetrics, ?> theoreticalSensitivityMetrics = getMetricsFile();
+            log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions.");
+            List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION);
+            theoreticalSensitivityMetrics.addAllMetrics(tsm);
+            theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
+        }
+
         return 0;
     }
 

src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java

@@ -32,7 +32,7 @@ import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.StringUtil;
-import org.broadinstitute.barclay.argparser.BetaFeature;
+import org.broadinstitute.barclay.argparser.ExperimentalFeature;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.PicardException;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -46,7 +46,7 @@ import java.io.File;
 import java.util.List;
 
 @DocumentedFeature
-@BetaFeature
+@ExperimentalFeature
 @CommandLineProgramProperties(
         summary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY + CollectWgsMetricsWithNonZeroCoverage.USAGE_DETAILS,
         oneLineSummary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY,
@@ -54,7 +54,7 @@ import java.util.List;
 )
 public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics {
 
-    static final String USAGE_SUMMARY = "(Experimental) Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  ";
+    static final String USAGE_SUMMARY = "Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  ";
     static final String USAGE_DETAILS = "This tool collects metrics about the percentages of reads that pass base- and mapping- quality " +
             "filters as well as coverage (read-depth) levels. Both minimum base- and mapping-quality values as well as the maximum " +
             "read depths (coverage cap) are user defined.  This extends CollectWgsMetrics by including metrics related only to sites" +