lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

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CutN fails when sequence begins with Ns

hloucks opened this issue · comments

Using seqtk version 1.4-r122 seqt fails to identify Ns at the beginning of the contig

Example

>test
NNNNNNNATCTA
>test2
AATTCNNNA

seqtk cutN -g -n1 test.fa
test2	5	8

seqtk gap -l 1 test.fa
test	0	7
test2	5	8

CutN identifies the stretch of Ns in the second contig but not if the first which begins with Ns. Seqtk gap works as expected.