Class: Bio::Ngs::Bwa::Aln

Inherits:

Object

Object
Bio::Ngs::Bwa::Aln

show all

Includes:: Command::Wrapper

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

Overview

Usage: bwa aln [options] <prefix> <in.fq>

Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04]

-o INT    maximum number or fraction of gap opens [1]
-e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]
-i INT    do not put an indel within INT bp towards the ends [5]
-d INT    maximum occurrences for extending a long deletion [10]
-l INT    seed length [32]
-k INT    maximum differences in the seed [2]
-m INT    maximum entries in the queue [2000000]
-t INT    number of threads [1]
-M INT    mismatch penalty [3]
-O INT    gap open penalty [11]
-E INT    gap extension penalty [4]
-R INT    stop searching when there are >INT equally best hits [30]
-q INT    quality threshold for read trimming down to 35bp [0]
-f FILE   file to write output to instead of stdout
-B INT    length of barcode
-L        log-scaled gap penalty for long deletions
-N        non-iterative mode: search for all n-difference hits (slooow)
-I        the input is in the Illumina 1.3+ FASTQ-like format
-b        the input read file is in the BAM format
-0        use single-end reads only (effective with -b)
-1        use the 1st read in a pair (effective with -b)
-2        use the 2nd read in a pair (effective with -b)
-Y        filter Casava-filtered sequences

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?