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

Inherits:
Object
  • Object
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?