public void readBlocks(InputStream is, int nBlocks) throws IOException {
LittleEndianDataInputStream lis = new LittleEndianDataInputStream(is);
for (int i = 0; i < nBlocks; i++) {
int compressionMethod = lis.read();
int contentType = lis.read();
int contentId = ITF8.readUnsignedITF8(lis);
int size = ITF8.readUnsignedITF8(lis);
int rawSize = ITF8.readUnsignedITF8(lis);
byte[] blockData = new byte[size];
lis.readFully(blockData);
blockData = uncompress(blockData, compressionMethod);
String tmp = new String(blockData);
if (major >= 3) {
int checksum = CramInt.int32(lis);
}
}
}
public void readContainerHeader(long position) throws IOException {
SeekableStream ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
ss.seek(position);
BufferedInputStream bis = new BufferedInputStream(ss);
int length = CramInt.int32(bis);
int refSeqId = ITF8.readUnsignedITF8(bis);
int startPos = ITF8.readUnsignedITF8(bis);
int alignmentSpan = ITF8.readUnsignedITF8(bis);
int nRecords = ITF8.readUnsignedITF8(bis);
int recordCounter = ITF8.readUnsignedITF8(bis);
int bases = ITF8.readUnsignedITF8(bis);
int nBlocks = ITF8.readUnsignedITF8(bis);
int[] landmarks = CramArray.array(bis);
if (major >= 3) {
int checksum = CramInt.int32(bis);
}
readBlocks(bis, nBlocks);
}
public void fromByteArray(final byte[] data) {
final ByteBuffer buf = ByteBuffer.wrap(data);
buf.order(ByteOrder.LITTLE_ENDIAN);
stopByte = buf.get();
externalId = ITF8.readUnsignedITF8(buf);
}