@Test
public void testEncodeDecode() throws Exception {
String testFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test.sam";
SAMReader reader = new SAMReader(testFile);
Iterator<PicardAlignment> inputAlignmentIterator = reader.iterator();
ArrayList<PicardAlignment> inputAlignmentList = new ArrayList<PicardAlignment>();
while (inputAlignmentIterator.hasNext()) {
PicardAlignment al = inputAlignmentIterator.next();
inputAlignmentList.add(al);
}
ByteArrayOutputStream bos = new ByteArrayOutputStream();
FeatureEncoder<PicardAlignment> alignmentEncoder = new SamAlignmentEncoder();
alignmentEncoder.encodeAll(bos, reader.iterator());
ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
FeatureDecoder<PicardAlignment> alignmentDecoder = new AlignmentDecoder();
Iterator<PicardAlignment> decodedAlignments = alignmentDecoder.decodeAll(bis, false);
int ind = 0;
while (decodedAlignments.hasNext()) {
Alignment act = decodedAlignments.next();
Alignment exp = inputAlignmentList.get(ind++);
TestUtils.assertFeaturesEqual(exp, act);
assertEquals(exp.getCigarString(), act.getCigarString());
}
assertEquals("Different number of alignments read in as out", inputAlignmentList.size(), ind);
}
