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

Inherits:
Object
  • Object
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?