// 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);
}
public BamListContainer(SerializedAlignmentContainer bamList)
{
_index = 0;
_bamList = bamList;
}
// This comparison operator is copied exactly from samtools.
public int Compare(SerializedBamAlignment a,
SerializedBamAlignment b,
SerializedAlignmentContainer alignmentContainerA,
SerializedAlignmentContainer alignmentContainerB)
{
int cmp = FileOrderCompare(a, b);
if (cmp != 0)
{
return(cmp);
}
// They're the same.
// Test of negative strand flag is not really necessary, because it is tested
// with cmp if getFlags, but it is left here because that is the way it was done
// in the past.
if (a.IsReverseStrand == b.IsReverseStrand)
{
cmp = -1 * a.MapQuality.CompareTo(b.MapQuality);
if (cmp != 0)
{
return(cmp);
}
if (alignmentContainerA != null && alignmentContainerB != null)
{
// When storing a large number of records, the names are stored in the byte
// array to avoid a lot of memory allocations.
cmp = SerializedAlignmentContainer.CompareNames(a, b, alignmentContainerA, alignmentContainerB);
}
else
{
cmp = string.CompareOrdinal(a.Name, b.Name);
}
if (cmp != 0)
{
return(cmp);
}
cmp = a.AlignmentFlag.CompareTo(b.AlignmentFlag);
if (cmp != 0)
{
return(cmp);
}
cmp = a.MateRefID.CompareTo(b.MateRefID);
if (cmp != 0)
{
return(cmp);
}
cmp = a.MatePosition.CompareTo(b.MatePosition);
if (cmp != 0)
{
return(cmp);
}
cmp = a.FragmentLength.CompareTo(b.FragmentLength);
return(cmp);
}
else
{
return(a.IsReverseStrand ? 1 : -1);
}
}
public BamAlignmentComparer(SerializedAlignmentContainer alignmentContainer = null) : base()
{
_alignmentContainer = alignmentContainer;
}
