blastn2snp problem

[lindenb]

blastn2snp problem

[lindenb]

I'm away from my code: try to change '3' to '2' (or "1" ?) in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java#L175 and recompile

[mrb20045]

Thanks. I modified the BlastNToSnp.java based on your suggestion and recompiled. But the problem is not fixed. there is another way ?

Best

[lindenb]

I've added a new option -n (int) try to run this tool with -n 0 1907242

[mrb20045]

Dear Pierre
Thanks for your great support. the problem is not fixed yet with your improvement. I recompiled and ran the software with -n 0. but in some cases mismatches are reported as two or three like:

1:213087129-213087330(+) gi|229627866 298 1 101 298 + T A 97 T A .
1:213087129-213087330(+) gi|229628918 115 1 101 113 + C A 159 C A .
1:213087129-213087330(+) gi|229630731 7 1 101 262 - TG CT 192 CA AG ..
1:213087129-213087330(+) gi|229631360 26 1 101 200 - TGG CCT 201 CCA AGG ...

Can you fixed the problem please ?
Thanks again for your help.

Best

[lindenb]

No, sorry I won't fix this; this is clearly not a SNV but a di/tri nucleotide change.
You can always try to remove the lines 204-209

jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java

Lines 204 to 209 in 1907242

	for(;;)
	{
	int k=hspMid.indexOf(' ', j);
	if(k==-1 || k-j> minGapSize) break;
	j=k+1;
	}

[mrb20045]

Thanks for your help. I removed the mentioned lines but the problem was not fixed. however i fixed it by my script. Thanks again for your support.

Best