updating the gradle version from 2.13 to 3.2.1 (#727)

updating the gradle version from 2.13 to 3.2.1
adding a settings.gradle file to define the project name

these changes make it possible to use htsjdk in a composite gradle build with other projects

build.gradle

@@ -136,7 +136,7 @@ task testSRA(type: Test) {
 
 task wrapper(type: Wrapper) {
     description = "Regenerate the gradle wrapper"
-    gradleVersion = '2.13'
+    gradleVersion = '3.2.1'
 }
 
 // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Fri May 13 14:00:35 EDT 2016
+#Tue Nov 29 15:10:15 EST 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-bin.zip

gradlew

@@ -161,4 +161,9 @@ function splitJvmOpts() {
 eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
 JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
 
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then
+  cd "$(dirname "$0")"
+fi
+
 exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"

settings.gradle

@@ -0,0 +1 @@
+rootProject.name =	"htsjdk"