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#!/usr/bin/env perl
use Modern::Perl;
use FindBin;
use lib "$FindBin::Bin/../lib";
use BioX::Map::CLIS;

our $VERSION = '0.0.12'; # VERSION:
# ABSTRACT: a tool used to mapping and compare mapping result

# PODNAME: biox_map


BioX::Map::CLIS->new_with_cmd;

1;

__END__

=pod

=encoding UTF-8

=head1 NAME

biox_map - a tool used to mapping and compare mapping result

=head1 VERSION

version 0.0.12

=head1 SYNOPSIS

biox_map command syntax:

  biox_map <command> [options] [arguments]

Commands

  map                 mapping one or more samples using bwa or soap
  compare             compare the result of bwa or soap
  mapcompare          a pipeline to mapping and compare result

See `biox_map --help` for the full documentation of biox_map, or

See `biox_map <command> --help` for detail description of the command

=head1 COMMAND: map

usage 1: using 2 cpu cores to map one file

  biox_map map -i in.fastq -g hg19.fa -o out.txt -p 2

usage 2: batch mapping parallel, run 3 samples parallel with each one using 2 cpu

  biox_map map -I indir -g hg19.fa -O outdir -p 2 -P 3

=head1 COMMAND: compare

useage: all mapping result stored in indir. suffix of soap result is '.soap'[default:.soap] and suffix of bwa result is '.sam'[default: .bwa].

  biox_map compare -i indir -o summary.txt -s soap -b sam