Class: Bio::Ngs::Bwa::Bwasw

Inherits:

Object

Object
Bio::Ngs::Bwa::Bwasw

show all

Includes:: Command::Wrapper

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

Overview

Usage: bwa bwasw [options] <target.prefix> <query.fa> [query2.fa]

Options: -a INT score for a match [1] -b INT mismatch penalty [3] -q INT gap open penalty [5] -r INT gap extension penalty [2]

    -t INT   number of threads [1]

    -w INT   band width [50]
    -m FLOAT mask level [0.50]

    -T INT   score threshold divided by a [30]
    -s INT   maximum seeding interval size [3]
    -z INT   Z-best [1]
    -N INT   # seeds to trigger reverse alignment [5]
    -c FLOAT coefficient of length-threshold adjustment [5.5]
    -H       in SAM output, use hard clipping rather than soft
    -f FILE  file to output results to instead of stdout

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?