public BamReaderContainer(Stream inStream, string filename)
{
_bamReader = new BamReader();
_bamReader.Open(inStream);
_filename = filename;
_currentBamAlignment = new BamAlignment();
_currentSerializedAlignment = new SerializedBamAlignment();
MoveToNextRecord();
}
public void write(BamWriter writer,
int index)
{
SerializedBamAlignment alignment = _bamAlignmentList[index];
byte[] byteArray = null;
int smallOffset = 0;
_serializedAlignments.GetByteArrayAndOffset(alignment.SerializedOffset, ref byteArray, ref smallOffset);
writer.Write(byteArray, (uint)alignment.SerializedSize, smallOffset);
}
public override bool Equals(Object obj)
{
// Check for null values and compare run-time types.
if (obj == null || GetType() != obj.GetType())
{
return(false);
}
SerializedBamAlignment other = (SerializedBamAlignment)obj;
return(this == other);
}
// Avoid string allocations by iterating over the internal byte array.
public static int CompareNames(SerializedBamAlignment alignment1,
SerializedBamAlignment alignment2,
SerializedAlignmentContainer alignmentContainer1,
SerializedAlignmentContainer alignmentContainer2)
{
byte[] byteArray1 = null;
int offset1 = 0;
alignmentContainer1._serializedAlignments.GetByteArrayAndOffset(
alignment1.SerializedOffset,
ref byteArray1,
ref offset1);
byte[] byteArray2 = null;
int offset2 = 0;
alignmentContainer2._serializedAlignments.GetByteArrayAndOffset(
alignment2.SerializedOffset,
ref byteArray2,
ref offset2);
// The name starts at the 36th byte
UInt32 alignmentNamePos = 36;
offset1 += (int)alignmentNamePos;
offset2 += (int)alignmentNamePos;
int initOffset1 = offset1;
while (byteArray1[offset1] != '\0' && byteArray1[offset1] == byteArray2[offset2])
{
++offset1;
++offset2;
}
if (byteArray1[offset1] < byteArray2[offset2])
{
return(-1);
}
if (byteArray1[offset1] > byteArray2[offset2])
{
return(1);
}
return(0);
}
