@Test
public void test2() throws IOException {
SAMFileReader r =
new SAMFileReader(
new File("c:/temp/HG00096.mapped.illumina.mosaik.GBR.exome.20110411.chr20.bam"));
SAMRecordIterator iterator = r.iterator();
CompressionHeaderFactory.HuffmanParamsCalculator c = new HuffmanParamsCalculator();
String[] names = new String[100000];
for (int i = 0; i < names.length && iterator.hasNext(); i++) {
names[i] = iterator.next().getReadName();
c.add(names[i].length());
}
iterator.close();
r.close();
c.calculate();
int[] values = c.values();
int[] lens = c.bitLens();
System.out.println(Arrays.toString(values));
System.out.println(Arrays.toString(lens));
EncodingParams params = HuffmanIntegerEncoding.toParam(values, lens);
HuffmanIntegerEncoding e = new HuffmanIntegerEncoding();
e.fromByteArray(params.params);
BitCodec<Integer> codec = e.buildCodec(null, null);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
DefaultBitOutputStream bos = new DefaultBitOutputStream(baos);
for (int i = 0; i < names.length; i++) {
codec.write(bos, names[i].length());
}
bos.close();
codec = e.buildCodec(null, null);
ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
DefaultBitInputStream bis = new DefaultBitInputStream(bais);
for (int i = 0; i < names.length; i++) {
int v = codec.read(bis);
if (v != names[i].length()) fail("Mismatch: " + v + " vs " + names[i].length());
}
}
@Test
public void test() throws IOException {
int[] values = new int[] {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12};
int[] lens = new int[] {1, 2, 4, 4, 5, 5, 6, 6, 7, 7, 7, 8, 8};
CanonicalHuffmanIntegerCodec c = new CanonicalHuffmanIntegerCodec(values, lens);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
DefaultBitOutputStream bos = new DefaultBitOutputStream(baos);
for (int b : values) {
c.write(bos, b);
}
bos.close();
ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
DefaultBitInputStream bis = new DefaultBitInputStream(bais);
for (int b : values) {
int v = c.read(bis);
if (v != b) fail("Mismatch: " + v + " vs " + b);
}
}