deprecating overloads makeCRAMWriter with mixed Path/File (#1150)

* Deprecating overloads of SAMFileWriterFactory.makeCRAMWriter and .makeWriter that took a mix of Path and File as inputs.
  These were needed when we supported Path for the CRAM but not the reference.

* Removing one overload that seems redundant and hasn't been in any htsjdk release yet.

src/main/java/htsjdk/samtools/SAMFileWriterFactory.java

@@ -452,7 +452,7 @@ public SAMFileWriter makeSAMOrBAMWriter(final SAMFileHeader header, final boolea
      *
      */
     public SAMFileWriter makeWriter(final SAMFileHeader header, final boolean presorted, final File outputFile, final File referenceFasta) {
-        return makeWriter(header, presorted, null == outputFile ? null : outputFile.toPath(), referenceFasta);
+        return makeWriter(header, presorted, null == outputFile ? null : outputFile.toPath(), null == referenceFasta ? null : referenceFasta.toPath());
     }
 
     /**
@@ -464,8 +464,9 @@ public SAMFileWriter makeWriter(final SAMFileHeader header, final boolean presor
      * @param outputPath where to write the output.  Must end with .sam, .bam or .cram.
      * @param referenceFasta reference sequence file
      * @return SAMFileWriter appropriate for the file type specified in outputPath
-     *
+     * @deprecated since 6/18, use {@link #makeWriter(SAMFileHeader, boolean, Path, Path)} instead
      */
+    @Deprecated
     public SAMFileWriter makeWriter(final SAMFileHeader header, final boolean presorted, final Path outputPath, final File referenceFasta) {
         return makeWriter(header, presorted, outputPath, null == referenceFasta ? null : referenceFasta.toPath());
     }
@@ -550,9 +551,12 @@ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final File outp
      * @param referenceFasta reference sequence file
      * @return CRAMFileWriter
      *
+     * @deprecated since 6/18, prefer {@link #makeWriter(SAMFileHeader, boolean, Path, Path)} for creating bam/cram writers
+     * however {@link #makeCRAMWriter(SAMFileHeader, boolean, Path, Path)} is the direct replacement for this method
      */
+    @Deprecated
     public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final Path outputPath, final File referenceFasta) {
-        return createCRAMWriterWithSettings(header, true, outputPath, null == referenceFasta ? null : referenceFasta.toPath());
+        return makeCRAMWriter(header, true, outputPath, null == referenceFasta ? null : referenceFasta.toPath());
     }
 
     /**
@@ -568,7 +572,7 @@ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final Path outp
      *
      */
     public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile, final File referenceFasta) {
-        return makeCRAMWriter(header, presorted, outputFile.toPath(), referenceFasta);
+        return makeCRAMWriter(header, presorted, outputFile.toPath(),  null == referenceFasta ? null : referenceFasta.toPath());
     }
 
 
@@ -583,25 +587,13 @@ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean p
      * @param referenceFasta reference sequence file
      * @return CRAMFileWriter
      *
-     */
-    public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean presorted, final Path output, final File referenceFasta) {
-        return createCRAMWriterWithSettings(header, presorted, output, null == referenceFasta ? null : referenceFasta.toPath());
-    }
-
-    /**
-     * Create a CRAMFileWriter on an output file. Requires input record to be presorted to match the
-     * sort order defined by the input header.
-     *
-     * Note: does not honor factory settings for USE_ASYNC_IO.
-     *
-     * @param header entire header. Sort order is determined by the sortOrder property of this arg.
-     * @param outputPath where to write the output.  Must end with .sam, .bam or .cram.
-     * @param referenceFasta reference sequence file
-     * @return CRAMFileWriter
+     * @deprecated since 6/18, prefer {@link #makeWriter(SAMFileHeader, boolean, Path, Path)} for creating bam/cram writers
+     * however {@link #makeCRAMWriter(SAMFileHeader, boolean, Path, Path)} is the direct replacement for this method
      *
      */
-    public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final Path outputPath, final Path referenceFasta) {
-        return createCRAMWriterWithSettings(header, true, outputPath, referenceFasta);
+    @Deprecated
+    public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean presorted, final Path output, final File referenceFasta) {
+        return makeCRAMWriter(header, presorted, output, null == referenceFasta ? null : referenceFasta.toPath());
     }
 
     /**

src/test/java/htsjdk/samtools/CRAMComplianceTest.java

@@ -392,7 +392,7 @@ private void writeRecordsToPath (
         // tests to fail since it can change the order of some unmapped reads - this is allowed
         // by the spec since the order is arbitrary for unmapped.
         try (final SAMFileWriter writer = new SAMFileWriterFactory()
-            .makeWriter(samHeader, true, targetPath, referenceFile)) {
+            .makeWriter(samHeader, true, targetPath, referenceFile.toPath())) {
             for (SAMRecord rec : recs) {
                 writer.addAlignment(rec);
             }

src/test/java/htsjdk/samtools/SAMFileWriterFactoryTest.java

@@ -337,7 +337,7 @@ public void testMakeWriterPath(String extension) throws Exception {
             Files.deleteIfExists(outputPath);
             final SAMFileHeader header = new SAMFileHeader();
             final SAMFileWriterFactory factory = createWriterFactoryWithOptions(header);
-            final File referenceFile = new File(TEST_DATA_DIR, "hg19mini.fasta");
+            final Path referenceFile = new File(TEST_DATA_DIR, "hg19mini.fasta").toPath();
 
             int nRecs;
             try (final SAMFileWriter samWriter = factory.makeWriter(header, false, outputPath, referenceFile)) {