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