seqtk cutN tolerates non-N bases in its output

[charles-plessy]

Description of the bug

I just figured out that seqtk cutN tolerates non-N bases in its output. In the example below you can see that it reports the range 229-610, which is not exclusively made of Ns. Worse, it reports overlapping ranges, which confuses tools. Setting a high penalty with the -p option apparently solves the problem.

As I misunderstood how seqtk cutN works, the regions maked in pink in the dotplots may be overly broad. To resolve this issue I need either:

• Set -p to a value that I know is always high enough, or
• replace seqtk with an awk script.

Command used and terminal output

cat > test.fa <<__END__
>test
TNNNNNNNNNNNNNNNNTTATTTAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCACTTTTAATTNN
NNNNNNNNNNNCTATTTAATCCTTCTTTTTCTTTAATCTTAAAATTATCNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNTTATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNTAAGATT
TATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNATNNNNNNNNNNNNNNNNNNNATTNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNAGCTCTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNTAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATA
ATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
__END__
$ seqtk cutN -g -n 1 test.fa 
test	1	17
test	26	166
test	178	191
test	229	610
test	612	631
test	229	665
test	675	740
test	745	776
test	783	831
$ seqtk cutN -g -n 1 -p 10000 test.fa 
test	1	17
test	26	166
test	178	191
test	229	304
test	309	396
test	397	413
test	424	495
test	499	610
test	612	631
test	634	665
test	675	740
test	745	776
test	783	831