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CutN fails when sequence begins with Ns #211

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hloucks opened this issue Apr 19, 2024 · 0 comments
Open

CutN fails when sequence begins with Ns #211

hloucks opened this issue Apr 19, 2024 · 0 comments

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@hloucks
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hloucks commented Apr 19, 2024

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.
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@hloucks