/// <summary>
/// Writes speciied BAMIndex data.
/// </summary>
/// <param name="bamIndex">BAMIndex instance to write.</param>
public void Write(BAMIndex bamIndex)
{
if (bamIndex == null)
{
throw new ArgumentNullException("bamIndex");
}
if (_stream == null)
{
throw new InvalidOperationException(Resource.BAM_CantUseBAMIndexStreamDisposed);
}
byte[] arrays = new byte[20];
byte[] magic = new byte[] { 66, 65, 73, 1 };
Write(magic, 0, 4);
arrays = Helper.GetLittleEndianByteArray(bamIndex.RefIndexes.Count);
Write(arrays, 0, 4);
for (Int32 refindex = 0; refindex < bamIndex.RefIndexes.Count; refindex++)
{
BAMReferenceIndexes bamindices = bamIndex.RefIndexes[refindex];
arrays = Helper.GetLittleEndianByteArray(bamindices.Bins.Count);
Write(arrays, 0, 4);
for (Int32 binIndex = 0; binIndex < bamindices.Bins.Count; binIndex++)
{
Bin bin = bamindices.Bins[binIndex];
arrays = Helper.GetLittleEndianByteArray(bin.BinNumber);
Write(arrays, 0, 4);
arrays = Helper.GetLittleEndianByteArray(bin.Chunks.Count);
Write(arrays, 0, 4);
for (Int32 chunkIndex = 0; chunkIndex < bin.Chunks.Count; chunkIndex++)
{
Chunk chunk = bin.Chunks[chunkIndex];
arrays = GetBAMOffsetArray(chunk.ChunkStart);
Write(arrays, 0, 8);
arrays = GetBAMOffsetArray(chunk.ChunkEnd);
Write(arrays, 0, 8);
}
}
arrays = Helper.GetLittleEndianByteArray(bamindices.LinearOffsets.Count);
Write(arrays, 0, 4);
for (Int32 offsetIndex = 0; offsetIndex < bamindices.LinearOffsets.Count; offsetIndex++)
{
FileOffset value = bamindices.LinearOffsets[offsetIndex];
arrays = GetBAMOffsetArray(value);
Write(arrays, 0, 8);
}
_stream.Flush();
}
_stream.Flush();
}
/// <summary>
/// Returns BAMIndex instance by parsing BAM index source.
/// </summary>
public BAMIndex Read()
{
if (_stream == null)
{
throw new InvalidOperationException(Resource.BAM_CantUseBAMIndexStreamDisposed);
}
BAMIndex bamIndex = new BAMIndex();
byte[] arrays = new byte[20];
Read(arrays, 0, 4);
if (arrays[0] != 66 || arrays[1] != 65 || arrays[2] != 73 || arrays[3] != 1)
{
throw new FormatException(Resource.BAM_InvalidIndexFile);
}
Read(arrays, 0, 4);
int n_ref = Helper.GetInt32(arrays, 0);
for (Int32 refindex = 0; refindex < n_ref; refindex++)
{
BAMReferenceIndexes bamindices = new BAMReferenceIndexes();
bamIndex.RefIndexes.Add(bamindices);
Read(arrays, 0, 4);
int n_bin = Helper.GetInt32(arrays, 0);
for (Int32 binIndex = 0; binIndex < n_bin; binIndex++)
{
Bin bin = new Bin();
bamindices.Bins.Add(bin);
Read(arrays, 0, 4);
bin.BinNumber = Helper.GetUInt32(arrays, 0);
Read(arrays, 0, 4);
int n_chunk = Helper.GetInt32(arrays, 0);
for (Int32 chunkIndex = 0; chunkIndex < n_chunk; chunkIndex++)
{
Chunk chunk = new Chunk();
bin.Chunks.Add(chunk);
Read(arrays, 0, 8);
chunk.ChunkStart = GetBAMOffset(arrays, 0);
Read(arrays, 0, 8);
chunk.ChunkEnd = GetBAMOffset(arrays, 0);
}
}
Read(arrays, 0, 4);
int n_intv = Helper.GetInt32(arrays, 0);
for (Int32 offsetIndex = 0; offsetIndex < n_intv; offsetIndex++)
{
FileOffset value;
Read(arrays, 0, 8);
value = GetBAMOffset(arrays, 0);
bamindices.LinearOffsets.Add(value);
}
}
return(bamIndex);
}
