comparison CoverageReport.pl @ 25:6cb012c8497a draft

Added BED format check before collapsing regions.

24:fd788f9db899

	$tarfile = "$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;

25:6cb012c8497a

	$tarfile = "$wd/Results.tar.gz";
}

## 0. Collapse overlapping target regions.
if (defined($opts{'T'})) {
	## check BED format. Must have 6 cols if using this.
	my $head = `head -n 1 $opts{'t'}`;
	chomp;
	my @c = split(/\t/,$head);
	if (scalar(@c) < 6) {
		die("Targets BED file must be in 6-column format for collapsings. See tool documentation for more info.\n");
	}
	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;