# 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 # 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.