/ 
App-Sandy-0.25
River stage zero No dependents
/ App::Sandy::Command::Quality::Add

NAME

App::Sandy::Command::Quality::Add - quality subcommand class. Add a quality profile to the database.

VERSION

version 0.25

SYNOPSIS

sandy quality add -q <entry name> [-s <source>] [-e <error>] [-1] FILE

Arguments:
 a file (fastq or a file with quality entries only)

Mandatory options:
 -q, --quality-profile    a quality-profile name

Options:
 -h, --help               brief help message
 -H, --man                full documentation
 -v, --verbose            print log messages
 -s, --source             quality-profile source detail for database
 -1, --single-molecule    constraint to single-molecule sequencing
                          (as Pacbio and Nanopore)
 -e, --sequencing-error   sequencing error rate
                          [default:"0.001"; Number]

DESCRIPTION

Add a new quality-profile to the database. The profile will be generated from the quality strings, which encode the phred-score in ASCII characters from 0x21 to 0x7e (lowest and highest qualities). So the valid characters are:

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

INPUT

The user must pass a file in fastq format or a file containing only the ASCII-encoded phred-scores, as in this example:

===> my_qualities.txt
BECGF@F@DEBIDBE@DCC?HFH?BBB?H@FEEIFDCCECCCIGDIDI?@?CCC?AE?EC?F?@FB;<9<>9:599=>7:57614,30,440&"!***)#
@DCGIDBDECIHIG@FII?G?GCAD@BFECDCEF?H?GIHE?@GEECBCIHCABAFHDFAHBEBEB:5575678=75>657673-14,.113#"()#&)$
F?B@@DFAHIDD?EBFADICBFABCBBAHFCGF@@@?DEIAIEAFCEADC?B@IB?BIEABIBG@C<:;96<968:>::;778,+0203-3,#&'$$#&!
HAAAB@AGAEHC@CHE?EGI?@GFDFFAABDEBHBCDEAA?@IHEBCD@A@HDGFBA?@GHEGIE?5>;>8=75;5<6:<:76,.23-3141#("$"'%"
CDHC@ADAF?ED?GFFCFBDEE?BDACCEE??DA@?F@ABI@BHGIGFGBBDDBCHHEAIACC@GH<5577:><88;95>9:7///++24.2)"(#%&%$
...

AUTHORS

  • Thiago L. A. Miller <tmiller@mochsl.org.br>

  • J. Leonel Buzzo <lbuzzo@mochsl.org.br>

  • Felipe R. C. dos Santos <fsantos@mochsl.org.br>

  • Helena B. Conceição <hconceicao@mochsl.org.br>

  • Rodrigo Barreiro <rbarreiro@mochsl.org.br>

  • Gabriela Guardia <gguardia@mochsl.org.br>

  • Fernanda Orpinelli <forpinelli@mochsl.org.br>

  • Rafael Mercuri <rmercuri@mochsl.org.br>

  • Rodrigo Barreiro <rbarreiro@mochsl.org.br>

  • Pedro A. F. Galante <pgalante@mochsl.org.br>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007