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Behaviour of the "--no-self" option #133

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ghost opened this issue Mar 13, 2018 · 2 comments
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Behaviour of the "--no-self" option #133

ghost opened this issue Mar 13, 2018 · 2 comments
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@ghost
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ghost commented Mar 13, 2018

Hello,
my question is simple. I am calling minimap2 like this
minimap2 -k15 -w5 -p0 -g10000 --no-self splitted.fa splitted.fa
Here is sample output

contig1125_size18652167_part_329	5000	19	4488	+	contig1125_size18652167_part_329	5000	227	4666	77	4469	0	tp:A:P	cm:i:13	s1:i:71	s2:i:71
contig1125_size18652167_part_329	5000	227	4666	+	contig1125_size18652167_part_329	5000	19	4488	77	4469	0	tp:A:S	cm:i:13	s1:i:71
contig1125_size18652167_part_329	5000	219	283	+	contig1125_size18652167_part_328	5000	3555	3619	53	64	0	tp:A:S	cm:i:10	s1:i:53
contig1125_size18652167_part_329	5000	4001	4074	-	contig1125_size18652167_part_3024	5000	1885	1957	50	73	0	tp:A:S	cm:i:4	s1:i:50
contig1125_size18652167_part_3024	5000	1885	1957	-	contig1125_size18652167_part_329	5000	4001	4074	50	73	12	tp:A:P	cm:i:4	s1:i:50	s2:i:0

Why is the first line reported, since it's a self-alignment? Is it because the alignment doesn't strictly span the 5000 bp of the contig?
Thank you
@lh3 lh3 added the question label Mar 13, 2018
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lh3 commented Mar 13, 2018

No, it is not, because coordinates are different. BTW, you should update to more recent versions. "--no-self" is now an alias of "-D". The man page gives a better explanation.

@lh3 lh3 closed this as completed Mar 13, 2018
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lh3 commented Mar 13, 2018

PS: see option"-D" here.

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