Tile comparison in clumpify

[isinaltinkaya]

Hi,

I have some questions regarding this code to make sure I understood it correctly.

For a given read with QNAME xxx:yyy:zz:6:1205:5221:72504, following the naming conventions for NovaSeq 6000: lane=6, surface=1,swath=2,tile=05,x=522,y=72504
I think you use 1205 as 'tile' in your code. Is this correct?

If so, for another read with QNAME ..:6:1305:5000:5000, you would then define tile as 1305. When you use

BBMap/current/cluster/ClusterTools.java

Line 147 in a9ceda0

double d=Tools.absdif((double)a[i], (double)b[i]);

, since you don't use absDif from ClusterTools (

BBMap/current/cluster/ClusterTools.java

Line 128 in a9ceda0

static final float absDif(float[] a, float[] b){

) but use absdif from shared tools(

BBMap/current/shared/Tools.java

Line 2907 in a9ceda0

public static int absdif(int a, int b) {

), it would return 100. So if it is on the same tile (05) but different swaths (2,3) it would not continue. Thus it will only treat duplicates from adjacent tiles as cluster duplicates, not from adjacent swaths. Is this correct?

Thank you!