NAME
BioX::Map - map read to genome with bwa and soap
VERSION
version 0.0.12
SYNOPSIS
use BioX::Map;
my $bm = BioX::Map->new(
infile => "in.fastq",
out_prefix => 'out',
genome => 'ref.fa',
);DESCRIPTION
This module aim to wrap bwa and soap, and statistic result
Attributes
infile
the fastq file
indir
The dir that include fastq file. The priority is higher than infile
outfile
path of outfile which could include path
outdir
outdir of mapping result
force_index
index genome before mapping
mismatch
set mismatch allowed in mapping
genome
path of genome file
tool
mapping software. Enum['bwa', 'soap']
bwa
path of bwa
soap
path of soap
soap_index
path of 2bwt-builder
process_tool
process of mapping software
process_sample
how many samples are processed parallel
METHODS
exist_index
check whether genome index exists
create_index
create genome index before mapping
_map_one
wrap mapping software
map
process one or more samples
statis_result
statis mapping result
AUTHOR
Yan Xueqing <yanxueqing621@163.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2016 by Yan Xueqing.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.