PicardTask to use the Intel deflater/inflater only if safe, by default

core/src/main/scala/dagr/core/cmdline/DagrCoreMain.scala

@@ -43,6 +43,48 @@ import dagr.core.tasksystem.Pipeline
 import scala.collection.mutable.ListBuffer
 import scala.util.{Failure, Success}
 
+
+/** A little class so that we don't have to rely on SystemUtils from org.apache.commons:commons-lang3.
+  *
+  * This implementation is duplicated from `com.fulcrumgenomics.cmdline.SystemUtils`.
+  */
+private[dagr] object SystemUtils {
+  /** The OS name prefixes for Linux */
+  private val LinuxNamePrefixes: Seq[String] = Seq("Linux", "LINUX")
+  /** The OS name prefixes for Mac */
+  private val MacNamePrefixes: Seq[String]   = Seq("Mac")
+  /** The current OS name. */
+  private val OsName: Option[String]         = getSystemProperty("os.name")
+  /** The current OS architecture */
+  private val OsArch: Option[String]         = getSystemProperty("os.arch")
+  /** The current OS version */
+  private val OsVersion: Option[String]      = getSystemProperty("os.version")
+
+  /** Gets a system property.  Returns None if not found or not allowed to look at. */
+  private def getSystemProperty(property: String): Option[String] = {
+    try {
+      Option(System.getProperty(property))
+    } catch { case _: SecurityException => None } // not allowed to look at this property
+  }
+
+  /** True if this OS is Linux, false otherwise. */
+  private val IsOsLinux: Boolean = LinuxNamePrefixes.exists(prefix => OsName.exists(_.startsWith(prefix)))
+  /** True if this OS is Mac, false otherwise. */
+  private val IsOsMac: Boolean   = MacNamePrefixes.exists(prefix => OsName.exists(_.startsWith(prefix)))
+  /** Returns true if the architecture is the given name, false otherwise. */
+  private def IsOsArch(name: String): Boolean = OsArch.contains(name)
+  /** Returns true if the operating system version starts with the given version string, false otherwise. */
+  private def IsOsVersion(prefix: String): Boolean = OsVersion.exists(_.startsWith(prefix))
+
+  /** True if the current system supports the Intel Inflater and Deflater, false otherwise. */
+  val IntelCompressionLibrarySupported: Boolean = {
+    if (!SystemUtils.IsOsLinux && !SystemUtils.IsOsMac) false
+    else if (SystemUtils.IsOsArch("ppc64le")) false
+    else if (SystemUtils.IsOsMac && SystemUtils.IsOsVersion("10.14.")) false // FIXME: https://github.com/Intel-HLS/GKL/issues/101
+    else true
+  }
+}
+
 object DagrCoreMain extends Configuration {
   /** The packages we wish to include in our command line **/
   protected def getPackageList: List[String] = {

tasks/src/main/scala/dagr/tasks/picard/PicardTask.scala

@@ -25,6 +25,7 @@ package dagr.tasks.picard
 
 import java.nio.file.Path
 
+import dagr.core.cmdline.SystemUtils
 import dagr.core.config.Configuration
 import dagr.core.execsystem.{Cores, Memory}
 import dagr.core.tasksystem.{FixedResources, ProcessTask}
@@ -48,6 +49,8 @@ object PicardTask {
   * @param useAdvancedGcOptions use advanced garbage collection parameters.
   * @param validationStringency set the default validation stringency for Picard.
   * @param useAsyncIo true if we are to use asynchronous IO, false otherwise.
+  * @param useJdkDeflater true if we are to use the JDK deflater, false if we are to use an alternate deflater (Intel).
+  * @param useJdkInflater true if we are to use the JDK inflater, false if we are to use an alternate inflater (Intel).
   * @param compressionLevel the compress level to use.
   * @param createIndex true if we are to create an index, false otherwise.
   * @param createMd5File true if we are to create an Md5 file, false otherwise.
@@ -57,7 +60,8 @@ abstract class PicardTask(var jvmArgs: List[String] = Nil,
                           var useAdvancedGcOptions: Boolean = true,
                           var validationStringency: Option[ValidationStringency] = Some(ValidationStringency.SILENT),
                           var useAsyncIo: Boolean = false,
-                          var useJdkInflater: Option[Boolean] = None,
+                          var useJdkDeflater: Option[Boolean] = Some(!SystemUtils.IntelCompressionLibrarySupported),
+                          var useJdkInflater: Option[Boolean] = Some(!SystemUtils.IntelCompressionLibrarySupported),
                           var compressionLevel: Option[Int] = None,
                           var createIndex: Option[Boolean] = Some(true),
                           var createMd5File: Option[Boolean] = None,
@@ -91,6 +95,7 @@ abstract class PicardTask(var jvmArgs: List[String] = Nil,
     validationStringency.foreach(v => buffer.append("VALIDATION_STRINGENCY=" + v.name()))
     createIndex.foreach(c => buffer.append("CREATE_INDEX=" + c))
     createMd5File.foreach(c =>  buffer.append("CREATE_MD5_FILE=" + c))
+    useJdkDeflater.foreach(u => buffer.append("USE_JDK_DEFLATER=" + u))
     useJdkInflater.foreach(u => buffer.append("USE_JDK_INFLATER=" + u))
 
     addPicardArgs(buffer)
@@ -116,6 +121,9 @@ abstract class PicardTask(var jvmArgs: List[String] = Nil,
     this
   }
 
+  /** Sets whether we use the JDK deflater or not. */
+  def withJdkDeflater(deflate: Boolean = true) : this.type = { this.useJdkDeflater = Some(deflate); this; }
+
   /** Sets whether we use the JDK inflater or not. */
   def withJdkInflater(inflate: Boolean = true) : this.type = { this.useJdkInflater = Some(inflate); this; }
 }