Changes to FastaReferenceWriter

build.gradle

@@ -109,6 +109,7 @@ test {
         exclude "broken"
         exclude "defaultReference"
         exclude "ftp"
+        exclude "http"
         exclude "sra"
         exclude "ena"
 
@@ -127,11 +128,12 @@ task testFTP(type: Test) {
 }
 
 task testExternalApis(type: Test) {
-    description = "Run the SRA and ENA tests (tests that interact with external APIs)"
+    description = "Run the SRA, ENA, and HTTP tests (tests that interact with external APIs)"
     jvmArgs += '-Dsamjdk.sra_libraries_download=true'
 
     tags {
         include "sra"
+        include "http"
         include "ena"
         exclude "slow"
         exclude "broken"

src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java

@@ -25,7 +25,8 @@
 package htsjdk.samtools;
 
 import htsjdk.samtools.util.LineReader;
-import java.io.BufferedWriter;
+
+import java.io.Writer;
 
 /**
  * "On the fly" codec SAMSequenceDictionaryCodec.
@@ -67,7 +68,7 @@ public class SAMSequenceDictionaryCodec {
 
     private final SAMTextHeaderCodec codec;
 
-    public SAMSequenceDictionaryCodec(final BufferedWriter writer) {
+    public SAMSequenceDictionaryCodec(final Writer writer) {
         codec = new SAMTextHeaderCodec();
         codec.setmFileHeader(EMPTY_HEADER);
         codec.setWriter(writer);

src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java

@@ -62,7 +62,7 @@ public class SAMTextHeaderCodec {
     private ValidationStringency validationStringency = ValidationStringency.SILENT;
 
     // These attributes are populated when generating text
-    private BufferedWriter writer;
+    private Writer writer;
 
     private static final String TAG_KEY_VALUE_SEPARATOR = ":";
     private static final char TAG_KEY_VALUE_SEPARATOR_CHAR = ':';
@@ -73,7 +73,7 @@ public class SAMTextHeaderCodec {
     public static final String COMMENT_PREFIX = HEADER_LINE_START + HeaderRecordType.CO.name() + FIELD_SEPARATOR;
     private static final Log log = Log.getInstance(SAMTextHeaderCodec.class);
 
-    void setWriter(final BufferedWriter writer) {
+    void setWriter(final Writer writer) {
         this.writer = writer;
     }
 

src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java

@@ -32,6 +32,7 @@
 
 import java.io.*;
 import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.*;
 
@@ -183,15 +184,14 @@ public final class FastaReferenceWriter implements AutoCloseable {
      * @param dictOutput  the (uncompressed) output stream to the dictFile, if requested, {@code null} if none should be generated.
      * @throws IllegalArgumentException if {@code fastaFile} is {@code null} or {@code basesPerLine} is 0 or negative.
      */
-    protected FastaReferenceWriter(final int basesPerLine,
+    FastaReferenceWriter(final int basesPerLine,
                                    final OutputStream fastaOutput,
                                    final OutputStream indexOutput,
                                    final OutputStream dictOutput) {
         this.defaultBasePerLine = basesPerLine;
         this.fastaStream = new CountingOutputStream(fastaOutput);
         this.indexWriter = indexOutput == null ? NullWriter.NULL_WRITER : new OutputStreamWriter(indexOutput, CHARSET);
-        final BufferedWriter dictWriter = new BufferedWriter(dictOutput == null ? NullWriter.NULL_WRITER : new OutputStreamWriter(dictOutput, CHARSET));
-        this.dictWriter = dictWriter;
+        this.dictWriter = dictOutput == null ? NullWriter.NULL_WRITER : new OutputStreamWriter(dictOutput, CHARSET);
         this.dictCodec = new SAMSequenceDictionaryCodec(dictWriter);
         this.dictCodec.encodeHeaderLine(false);
     }
@@ -441,7 +441,7 @@ private void writeDictEntry() {
      */
     public FastaReferenceWriter appendBases(final String basesBases)
             throws IOException {
-        return appendBases(basesBases.getBytes("ASCII"));
+        return appendBases(basesBases.getBytes(StandardCharsets.US_ASCII));
     }
 
     /**
@@ -592,20 +592,22 @@ private void assertIsNotClosed() {
      * </p>
      *
      * @throws IOException if such exception is thrown when closing output writers and output streams.
+     * @throws IllegalStateException if closing without writing any sequences or closing when writing a sequence is in progress
      */
+    @Override
     public void close() throws IOException {
-        try {
-            if (!closed) {
+        if (!closed) {
+            try {
                 closeSequence();
                 if (sequenceNames.isEmpty()) {
                     throw new IllegalStateException("no sequences were added to the reference");
                 }
+            } finally {
+                closed = true;
                 fastaStream.close();
                 indexWriter.close();
                 dictWriter.close();
             }
-        } finally {
-            closed = true;
         }
     }
 

src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java

@@ -26,6 +26,7 @@
 
 import htsjdk.utils.ValidationUtils;
 
+import java.io.BufferedOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.file.Files;
@@ -211,13 +212,13 @@ public FastaReferenceWriter build() throws IOException {
         checkBasesPerLine(basesPerLine);
 
         if (fastaFile != null) {
-            fastaOutput = Files.newOutputStream(fastaFile);
+            fastaOutput = new BufferedOutputStream(Files.newOutputStream(fastaFile));
         }
         if (indexFile != null) {
-            indexOutput = Files.newOutputStream(indexFile);
+            indexOutput = new BufferedOutputStream(Files.newOutputStream(indexFile));
         }
         if (dictFile != null) {
-            dictOutput = Files.newOutputStream(dictFile);
+            dictOutput = new BufferedOutputStream(Files.newOutputStream(dictFile));
         }
 
         return new FastaReferenceWriter(basesPerLine, fastaOutput, indexOutput, dictOutput);

src/test/java/htsjdk/samtools/util/HttpUtilsTest.java

@@ -8,12 +8,13 @@
 
 import htsjdk.HtsjdkTest;
 
+@Test(groups = "http")
 public class HttpUtilsTest extends HtsjdkTest {
     @DataProvider(name = "existing_urls")
     public Object[][] testExistingURLsData() {
         return new Object[][]{
             {"http://broadinstitute.github.io/picard/testdata/index_test.bam"},
-            {"http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree"}
+            {"http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README_using_1000genomes_cram.md"}
         };
     }