include cause when SAMFileWriterFactory rethrows exceptions (#1023)

*  RunTimeIOExceptions thrown in SAMFileWriterFactory now propagate the original IOException that caused them.

Author: jean-philippe-martin

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

@@ -32,7 +32,6 @@
 import htsjdk.samtools.util.zip.DeflaterFactory;
 
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.file.Files;
@@ -300,7 +299,7 @@ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean pre
             if (this.useAsyncIo) return new AsyncSAMFileWriter(ret, this.asyncOutputBufferSize);
             else return ret;
         } catch (final IOException ioe) {
-            throw new RuntimeIOException("Error opening file: " + outputPath.toUri());
+            throw new RuntimeIOException("Error opening file: " + outputPath.toUri(), ioe);
         }
     }
 
@@ -352,7 +351,7 @@ public SAMFileWriter makeSAMWriter(final SAMFileHeader header, final boolean pre
                                         samFlagFieldOutput);
             return initWriter(header, presorted, ret);
         } catch (final IOException ioe) {
-            throw new RuntimeIOException("Error opening file: " + outputPath.toUri());
+            throw new RuntimeIOException("Error opening file: " + outputPath.toUri(), ioe);
         }
     }
 
@@ -588,7 +587,7 @@ private CRAMFileWriter createCRAMWriterWithSettings(
                     indexOS = Files.newOutputStream(indexPath);
                 }
                 catch (final IOException ioe) {
-                    throw new RuntimeIOException("Error creating index file for: " + indexPath.toUri());
+                    throw new RuntimeIOException("Error creating index file for: " + indexPath.toUri(), ioe);
                 }
             }
         }
@@ -597,7 +596,7 @@ private CRAMFileWriter createCRAMWriterWithSettings(
             cramOS = IOUtil.maybeBufferOutputStream(Files.newOutputStream(outputFile), bufferSize);
         }
         catch (final IOException ioe) {
-            throw new RuntimeIOException("Error creating CRAM file: " + outputFile.toUri());
+            throw new RuntimeIOException("Error creating CRAM file: " + outputFile.toUri(), ioe);
         }
 
         final Path md5Path = IOUtil.addExtension(outputFile, ".md5");

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

@@ -29,9 +29,11 @@
 import htsjdk.samtools.cram.build.CramIO;
 import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.util.IOUtil;
+import htsjdk.samtools.util.RuntimeIOException;
 import java.nio.file.Path;
 import java.nio.file.Files;
 import java.nio.file.FileSystem;
+import java.nio.file.Paths;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -76,6 +78,17 @@ public void ordinaryPathWriterTest() throws Exception {
         }
     }
 
+    @Test()
+    public void pathWriterFailureMentionsCause() throws Exception {
+        try {
+            final Path outputPath = Paths.get("nope://no.txt");
+            createSmallBam(outputPath);
+            Assert.fail("Should have thrown a RuntimeIOException");
+        } catch (RuntimeIOException expected) {
+            Assert.assertTrue(expected.getCause().toString().contains("NoSuchFileException"));
+        }
+    }
+
     @Test(description="create a BAM in memory,  should start with GZipInputStream.GZIP_MAGIC")
     public void inMemoryBam()  throws Exception  {
     	ByteArrayOutputStream os=new ByteArrayOutputStream();