public static byte[][] LoadBGZippedCallsAndScores(string filePath, ulong startPosition, int clusterCount, out ulong EndPosition)
{
byte[][] callsAndScores = null;
using (BgzipReader reader = new BgzipReader(filePath))
{
if (startPosition > 0)
{
reader.Seek(startPosition);
}
else
{
reader.BlockOffset = 4;
}
byte[] buffer = reader.ReadBytes(clusterCount, out EndPosition);
if (callsAndScores == null)
{
callsAndScores = new byte[2][];
callsAndScores[0] = new byte[clusterCount];
callsAndScores[1] = new byte[clusterCount];
}
for (int clusterIndex = 0; clusterIndex < clusterCount; clusterIndex++)
{
if (buffer[clusterIndex] != 0) // can't be uncalled, so quality score must be > 0
callsAndScores[0][clusterIndex] = (byte)((buffer[clusterIndex] & 3) + 8);
else
callsAndScores[0][clusterIndex] = 0; // no-call reserved
callsAndScores[1][clusterIndex] = (byte)(buffer[clusterIndex] >> 2);
}
}
return callsAndScores;
}
private static byte[][] LoadBgzippedCallsAndScores(string filePath, ulong startPosition, int clusterCount, out ulong endPosition)
{
byte[][] callsAndScores;
using (BgzipReader reader = new BgzipReader(filePath))
{
reader.Seek(startPosition+4);
byte[] buffer = reader.ReadBytes(clusterCount, out endPosition);
callsAndScores = new byte[2][];
callsAndScores[0] = new byte[clusterCount];
callsAndScores[1] = new byte[clusterCount];
for (int clusterIndex = 0; clusterIndex < clusterCount; clusterIndex++)
{
if (buffer[clusterIndex] != 0) // can't be uncalled, so quality score must be > 0
callsAndScores[0][clusterIndex] = (byte) ((buffer[clusterIndex] & 3) + 8);
else
callsAndScores[0][clusterIndex] = 0; // no-call reserved
callsAndScores[1][clusterIndex] = (byte) (buffer[clusterIndex] >> 2);
}
}
return callsAndScores;
}