Added Io.readBytesFromResources() to read binary data.

src/main/scala/com/fulcrumgenomics/commons/io/Io.scala

@@ -27,6 +27,8 @@ import java.io._
 import java.nio.file.{Files, Path}
 
 import com.fulcrumgenomics.commons.CommonsDef._
+
+import scala.collection.mutable.ArrayBuffer
 import scala.io.Source
 
 /**
@@ -181,6 +183,13 @@ trait IoUtil {
   /** Creates an object that will asynchronously read character data from a stream and pipe it into a sink function. */
   def pipeStream(stream: InputStream, sink: String => Unit) : AsyncStreamSink = new AsyncStreamSink(stream, sink)
 
+  /** Private function to get an input stream from a resource, or fail if the resource doesn't exist. */
+  private def streamFromResource(name: String): InputStream = {
+    Seq(getClass.getResourceAsStream _, getClass.getClassLoader.getResourceAsStream _)
+      .flatMap(m => Option(m(name)))
+      .headOption.getOrElse(throw new IllegalArgumentException(s"Resource does not exist at path: $name"))
+  }
+
   /** Finds a resource with a given name on the classpath and produces an iterator of lines of text from the resource.
     *
     * The way resources are traditionally loaded from the class path via `Class.getResource()` and
@@ -191,17 +200,27 @@ trait IoUtil {
     *
     * The implementation here first tries `Class.getResource` and then `ClassLoader.getResource` to enable it to
     * find relative paths and also absolute paths with and without leading `/s`.
-    *
     */
   def readLinesFromResource(name: String): Iterator[String] = {
-    Seq(getClass.getResourceAsStream _, getClass.getClassLoader.getResourceAsStream _)
-      .flatMap(m => Option(m(name)))
-      .headOption match {
-        case None     =>
-          throw new IllegalArgumentException(s"Resource does not exist at path: $name")
-        case Some(in) =>
-          val stream = new BufferedInputStream(in, bufferSize)
-          Source.fromInputStream(stream).withClose(() => stream.safelyClose()).getLines
-    }
+    val stream = new BufferedInputStream(streamFromResource(name), bufferSize)
+    Source.fromInputStream(stream).withClose(() => stream.safelyClose()).getLines
+  }
+
+  /** Finds a resource with a given name on the classpath and produces an array of the bytes from the resource.
+    *
+    * The way resources are traditionally loaded from the class path via `Class.getResource()` and
+    * `ClassLoader.getResource()` have confusing behaviour.  Notably:
+    *
+    * * Class.getResource() interprets paths as relative, and requires a leading `/` to make them absolute
+    * * ClassLoader.getResource() interprets all paths a absolute and fails on leading `/`s
+    *
+    * The implementation here first tries `Class.getResource` and then `ClassLoader.getResource` to enable it to
+    * find relative paths and also absolute paths with and without leading `/s`.
+    */
+  def readBytesFromResource(name: String): Array[Byte] = {
+    val stream = new BufferedInputStream(streamFromResource(name), bufferSize)
+    val array = Iterator.continually(stream.read()).takeWhile(_ != -1).map(_.toByte).toArray
+    stream.safelyClose()
+    array
   }
 }

src/test/scala/com/fulcrumgenomics/commons/io/IoTest.scala

@@ -23,6 +23,7 @@
  */
 package com.fulcrumgenomics.commons.io
 
+import java.io.{BufferedOutputStream, FileOutputStream}
 import java.nio.file.{Files, Path, Paths}
 
 import com.fulcrumgenomics.commons.util.UnitSpec
@@ -186,4 +187,10 @@ class IoTest extends UnitSpec {
   it should "fail when the resource does not exist" in {
     an[IllegalArgumentException] should be thrownBy Io.readLinesFromResource("/path/does/not/exist.json")
   }
+
+  "Io.readBytesFromResource" should "correctly read binary data from a resource" in {
+    val expected = Range.inclusive(Byte.MinValue, Byte.MaxValue).map(_.toByte).toArray
+    val actual = Io.readBytesFromResource("/com/fulcrumgenomics/commons/io/to-bytes-from-resource-test.bin")
+    actual shouldBe expected
+  }
 }