@Test(description = "Write SAM records with null SAMFileHeader")
public void samNullHeaderRoundTrip() throws Exception {
final File input = new File(TEST_DATA_DIR, "roundtrip.sam");
final SamReader reader = SamReaderFactory.makeDefault().open(input);
final File outputFile = File.createTempFile("nullheader-out", ".sam");
outputFile.delete();
outputFile.deleteOnExit();
FileOutputStream os = new FileOutputStream(outputFile);
final SAMFileWriterFactory factory = new SAMFileWriterFactory();
final SAMFileWriter writer = factory.makeSAMWriter(reader.getFileHeader(), false, os);
for (SAMRecord rec : reader) {
rec.setHeader(null);
writer.addAlignment(rec);
}
writer.close();
os.close();
InputStream is = new FileInputStream(input);
String originalsam = IOUtil.readFully(is);
is.close();
is = new FileInputStream(outputFile);
String writtensam = IOUtil.readFully(is);
is.close();
Assert.assertEquals(writtensam, originalsam);
}
