Adding http-nio as a dependency (#1929)

* This is a plugin which provides HttpFileSystemProvider which allows connecting to http(s) paths
  through the nio Path and Files interfaces.
* Updating htsjdk to 4.1.0 which improves support for plugins lke this in Tribble.
* Adding an extremely simple test to show that http-nio is available

build.gradle

@@ -59,7 +59,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '4.0.2')
+final htsjdkVersion = System.getProperty('htsjdk.version', '4.1.0')
 dependencies {
     implementation('com.intel.gkl:gkl:0.8.11') {
         exclude module: 'htsjdk'
@@ -76,8 +76,10 @@ dependencies {
     implementation 'org.openjdk.nashorn:nashorn-core:15.4'
     implementation 'org.apache.commons:commons-lang3:3.12.0'
     implementation 'com.google.cloud:google-cloud-nio:0.127.0'
+    implementation 'org.broadinstitute:http-nio:1.1.0'
     implementation 'commons-io:commons-io:2.11.0'
 
+
     testImplementation 'org.testng:testng:7.7.0'
 }
 

src/test/java/picard/nio/HttpNioIntegrationTest.java

@@ -0,0 +1,17 @@
+package picard.nio;
+
+import htsjdk.samtools.util.IOUtil;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+
+public class HttpNioIntegrationTest {
+    @Test
+    public void testCanReadFromHttpsPath() throws IOException {
+        final String theWholeReadme = Files.readString(IOUtil.getPath("https://raw.githubusercontent.com/broadinstitute/picard/master/README.md"));
+        Assert.assertTrue(theWholeReadme.contains("Picard"));
+    }
+
+}

testdata/picard/util/BedToIntervalListTest/simple.bed

@@ -1,2 +1,3 @@
+
 chr1	100	2000
 chr1	3000	4000