@Test public void test_updateSubstitutionCodes() { final CramCompressionRecord record = new CramCompressionRecord(); final Substitution s = new Substitution(); s.setPosition(1); final byte refBase = 'A'; final byte readBase = 'C'; s.setBase(readBase); s.setReferenceBase(refBase); record.readFeatures = new ArrayList<>(); record.readFeatures.add(s); record.readLength = 2; final List<CramCompressionRecord> records = new ArrayList<>(); records.add(record); final long[][] frequencies = new long[256][256]; frequencies[refBase][readBase] = 1; SubstitutionMatrix matrix = new SubstitutionMatrix(frequencies); Assert.assertTrue(s.getCode() == -1); CompressionHeaderFactory.updateSubstitutionCodes(records, matrix); Assert.assertFalse(s.getCode() == -1); Assert.assertEquals(s.getCode(), matrix.code(refBase, readBase)); }
updateSubstitutionCodes(records, substitutionMatrix);
updateSubstitutionCodes(records, substitutionMatrix);