Ensure VCF output appends appropriate gzip termination blocks.

Several VCF writing commands were inconsistently in whether they
appended gzip termination blocks, producing warnings with third party
tools.

test/com/rtg/variant/cnv/segment/SegmentCliTest.java

@@ -25,6 +25,8 @@
 import com.rtg.util.io.TestDirectory;
 import com.rtg.util.test.FileHelper;
 
+import htsjdk.samtools.util.BlockCompressedInputStream;
+
 /**
  * Tests the corresponding class.
  */
@@ -82,10 +84,12 @@ public void testSimpleOperation() throws IOException {
       final File output = new File(dir, "output");
 
       // gc correction does not work well here because the regions are small, so turn it off
-      final MainResult result = MainResult.run(getCli(), "-t", reference.getPath(), "-o", output.getPath(), "--control", control.getPath(), "--case", sample.getPath(), "--sample", "foo", "-Z", "--beta", "0.1", "--Xgcbins", "0");
+      final MainResult result = MainResult.run(getCli(), "-t", reference.getPath(), "-o", output.getPath(), "--control", control.getPath(), "--case", sample.getPath(), "--sample", "foo", "--beta", "0.1", "--Xgcbins", "0");
       assertEquals(0, result.rc());
-      mNano.check("expected.unsegmented.bed", FileUtils.fileToString(new File(output, "unsegmented.bed")));
-      mNano.check("expected.segments.vcf", TestUtils.sanitizeVcfHeader(FileUtils.fileToString(new File(output, "segments.vcf"))));
+      final File vcf = new File(output, "segments.vcf.gz");
+      assertEquals(BlockCompressedInputStream.FileTermination.HAS_TERMINATOR_BLOCK, BlockCompressedInputStream.checkTermination(vcf));
+      mNano.check("expected.unsegmented.bed", FileHelper.gzFileToString(new File(output, "unsegmented.bed.gz")));
+      mNano.check("expected.segments.vcf", TestUtils.sanitizeVcfHeader(FileHelper.gzFileToString(vcf)));
       mNano.check("expected.summary.txt", FileUtils.fileToString(new File(output, "summary.txt")));
       mNano.check("expected.out.txt", result.out());
     }