comparison matching.pl @ 47:c75593f79aa9 draft

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46:ca05d68aca13

use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","time:s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'i'};

my $index=defined $opts{'index'} ? $opts{'index'} : "";
my $threads=defined $opts{'p'} ? $opts{'p'} : 1;


my $time=&Time();
if (defined $opts{'time'}) {
	$time=$opts{'time'};
}

my $mapdir=$fileout."/genome_match_".$time;
if(not -d $mapdir){
	mkdir $mapdir;
}
chdir $mapdir;
###check genome index

47:c75593f79aa9

use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'i'};

my $index=defined $opts{'index'} ? $opts{'index'} : "";
my $threads=defined $opts{'p'} ? $opts{'p'} : 1;


my $time=&Time();
my $mapdir=$fileout."/genome_match";
if(not -d $mapdir){
	mkdir $mapdir;
}
chdir $mapdir;
###check genome index