Class: Bio::Ngs::Fastx::QualityTrim

Inherits:

Object

Object
Bio::Ngs::Fastx::QualityTrim

show all

Includes:: Command::Wrapper

Defined in:: lib/bio/appl/ngs/fastx.rb

Overview

-h

This helpful help screen.

-t N

Quality threshold - nucleotides with lower

quality will be trimmed (from the end of the sequence).

-l N

Minimum length - sequences shorter than this (after trimming)

will be discarded. Default = 0 = no minimum length.

-z

Compress output with GZIP.

-i INFILE

FASTQ input file. default is STDIN.

-o OUTFILE

FASTQ output file. default is STDOUT.

-v

Verbose - report number of sequences.

If [-o] is specified,  report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.

Method Summary

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?