wip on #1614

This is more complicated than originally described because the file encoding isn't really described and java bytes include negative values.
EOF is triggered correctly, but it's also triggered on various potential characters which become negative values when they are truncated to byte.
It's unclear if this is meant to only read ASCII, ISO 8859-1, or UTF-8 but nothing outside of the ascii space works correctly.

Author: lbergelson

src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java

@@ -113,14 +113,14 @@ public final float readFloat() throws IOException {
 
     public String readString() throws IOException {
         ByteArrayOutputStream bis = new ByteArrayOutputStream(100);
-        byte b;
-        while ((b = (byte) in.read()) != 0) {
+        int b;
+        while ((b = in.read()) != 0) {
             if(b < 0) {
                 throw new EOFException();
             }
-            bis.write(b);
+            bis.write((byte)b);
         }
-        return new String(bis.toByteArray());
+        return bis.toString();
     }
 
 

src/test/java/htsjdk/tribble/util/LittleEndianInputStreamTest.java

@@ -0,0 +1,45 @@
+package htsjdk.tribble.util;
+
+import com.google.common.io.LittleEndianDataOutputStream;
+import htsjdk.HtsjdkTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.EOFException;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Files;
+
+import static org.testng.Assert.*;
+
+public class LittleEndianInputStreamTest extends HtsjdkTest {
+
+    @Test(expectedExceptions = EOFException.class)
+    public void testReadStringEOF() throws IOException {
+        final String emptyFile = "src/test/resources/htsjdk/tribble/util/string_with_extended_ascii_no_terminator.bin";
+        try(final LittleEndianInputStream in = new LittleEndianInputStream(new BufferedInputStream(new FileInputStream(emptyFile)))){
+          in.readString();
+        }
+    }
+
+    @Test
+    public void testReadStringWithExtendedCharacters() throws IOException {
+        final String emptyFile = "src/test/resources/htsjdk/tribble/util/string_with_extended_ascii_and_null_terminator.bin";
+        try(final LittleEndianInputStream in = new LittleEndianInputStream(new BufferedInputStream(new FileInputStream(emptyFile)))){
+            Assert.assertEquals(in.readString(), "very dràààààmatic and null terminated");
+        }
+    }
+
+
+    @Test(expectedExceptions = EOFException.class)
+    public void write() throws IOException {
+        final String emptyFile = "src/test/resources/htsjdk/tribble/util/string_with_extended_ascii_and_null_terminator.bin";
+        try(final LittleEndianDataOutputStream out = new LittleEndianDataOutputStream(new FileOutputStream(emptyFile))){
+            out.writeBytes("very dràààààmatic and null terminated\0");
+        }
+    }
+}