Class: Bio::Ngs::Bwa::Sampe

Inherits:

Object

Object
Bio::Ngs::Bwa::Sampe

show all

Includes:: Command::Wrapper

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

Overview

Usage: bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>

Options: -a INT maximum insert size [500]

-o INT   maximum occurrences for one end [100000]
-n INT   maximum hits to output for paired reads [3]
-N INT   maximum hits to output for discordant pairs [10]
-c FLOAT prior of chimeric rate (lower bound) [1.0e-05]
-f FILE  sam file to output results to [stdout]
-r STR   read group header line such as `@RG\tID:foo\tSM:bar' [null]
-P       preload index into memory (for base-space reads only)
-s       disable Smith-Waterman for the unmapped mate
-A       disable insert size estimate (force -s)

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?