search

tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
210 stars 41 forks source link

Uncorrect bedtools flag name fixed #33

Closed mariafiruleva closed 5 years ago

mariafiruleva commented 5 years ago

'-name+' has changed to '-name'

tseemann commented 5 years ago

@mariafiruleva for what version did this behaviour change?

% bedtools --version
bedtools v2.27.1
Options:
        -fi     Input FASTA file
        -fo     Output file (opt., default is STDOUT
        -bed    BED/GFF/VCF file of ranges to extract from -fi
        -name   Use the name field for the FASTA header
        -name+  Use the name field and coordinates for the FASTA header

Are you using the current version?

-name+ is a new option. See https://github.com/tseemann/barrnap/issues/29

mariafiruleva commented 5 years ago

No, I use bedtools v2.25.0. Sorry.

@mariafiruleva for what version did this behaviour change?

% bedtools --version
bedtools v2.27.1
Options:
        -fi     Input FASTA file
        -fo     Output file (opt., default is STDOUT
        -bed    BED/GFF/VCF file of ranges to extract from -fi
        -name   Use the name field for the FASTA header
        -name+  Use the name field and coordinates for the FASTA header

Are you using the current version?

-name+ is a new option. See #29

tseemann commented 5 years ago

@mariafiruleva the documentation states it needs 2.27 See: https://github.com/tseemann/barrnap#requirements I will try and add a check to ensure the user is using the correct version