comparison CoverageReport.pl @ 24:fd788f9db899 draft

Added (default) option to collapse repetitive bed files

23:a718420c834e

# m : (m)inimal Coverage threshold
# f : fraction of average as threshold
# n : sample (n)ame.
 

getopts('b:t:o:z:rsSALm:n:f:', \%opts) ;

# make output directory in (tmp) working dir
our $wd = "/tmp/Coverage.".int(rand(1000));
while (-d $wd) {
	$wd = "/tmp/Coverage.".int(rand(1000));
}
system("mkdir $wd");

## variables
our %commandsrun = ();

if (exists($opts{'z'})) {
	$tarfile = $opts{'z'};
}
else {
	$tarfile = "$wd/Results.tar.gz";
}

# 1. Global Summary => default
&GlobalSummary($opts{'b'}, $opts{'t'});

24:fd788f9db899

# m : (m)inimal Coverage threshold
# f : fraction of average as threshold
# n : sample (n)ame.
 

getopts('b:t:o:z:rsSALm:n:f:T', \%opts) ;

# make output directory in (tmp) working dir
our $wd = "/tmp/Coverage.".int(rand(1000));
while (-d $wd) {
	$wd = "/tmp/Coverage.".int(rand(1000));

}
system("mkdir $wd");

## variables
our %commandsrun = ();

if (exists($opts{'z'})) {
	$tarfile = $opts{'z'};
}
else {
	$tarfile = "$wd/Results.tar.gz";
}

## 0. Collapse overlapping target regions.
if (defined($opts{'T'})) {
	my $targets = $opts{'t'};
	my $tmptargets = "$wd/collapsedtargets.bed";
	system("sort -k1,1 -k2,2n $targets > $wd/sorted.targets.bed");
	system("bedtools merge -s -scores max -nms -i $wd/sorted.targets.bed > $tmptargets");
	$opts{'t'} = $tmptargets;
}

# 1. Global Summary => default
&GlobalSummary($opts{'b'}, $opts{'t'});