// opens BAM file
public void Open(string filename)
{
if (!File.Exists(filename))
{
throw new ApplicationException(string.Format("ERROR: The supplied BAM filename ({0}) does not exist.",
filename));
}
BamPath = filename;
// sanity check: make sure this is a GZIP file
ushort gzipMagicNumber;
using (BinaryReader checkReader = new BinaryReader(new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read)))
{
gzipMagicNumber = checkReader.ReadUInt16();
}
if (gzipMagicNumber != BamConstants.GzipMagicNumber)
{
throw new ApplicationException(string.Format(
"The input file ({0}) does not seem to be a BAM file. A GZIP magic number could not be found.", filename));
}
// open our file streams
try
{
BgzfFileStream = new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read);
_reader = new BinaryReader(BgzfFileStream);
}
catch (IOException e)
{
throw new ApplicationException(string.Format(
"ERROR: Unable to open the BAM file ({0}) for reading: {1}", filename, e.Message));
}
IsOpen = true;
// open the index file if it exists
string indexPath = string.Format("{0}.bai", filename);
if (_index.ReadIndex(indexPath))
{
_hasIndex = true;
}
LoadHeaderData();
LoadReferenceData();
// store file offset of first alignment
_alignmentsOffset = ((BlockAddress << 16) | ((long)BlockOffset & 0xFFFF));
}
// opens BAM file
public void Open(Stream inStream)
{
// sanity check: make sure this is a GZIP file
ushort gzipMagicNumber;
BgzfFileStream = inStream;
try
{
_reader = new BinaryReader(BgzfFileStream);
}
catch (IOException e)
{
throw new IOException(string.Format(
"ERROR: Unable to open the BAM file ({0}) for reading: {1}", BamPath, e.Message));
}
try
{
gzipMagicNumber = _reader.ReadUInt16();
if (gzipMagicNumber != BamConstants.GzipMagicNumber)
{
throw new InvalidDataException($"A GZIP magic number could not be found. Check BAM file {BamPath}");
}
}
catch (Exception e)
{
throw new IOException($"The input file ({BamPath}) does not seem to be a BAM file.", e);
}
inStream.Seek(0, SeekOrigin.Begin);
IsOpen = true;
// open the index file if it exists
string indexPath = string.Format("{0}.bai", BamPath);
if (!string.IsNullOrEmpty(BamPath) && _index.ReadIndex(indexPath))
{
_hasIndex = true;
}
LoadHeaderData();
LoadReferenceData();
// store file offset of first alignment
_alignmentsOffset = ((BlockAddress << 16) | ((long)BlockOffset & 0xFFFF));
}
