adding ability to handle multiple ligation junctions (d696dd12) · Commits · Chaos / chaos.juicer

SLURM/scripts/statistics.pl

+6 −1

Changes for SLURM/scripts/statistics.pl: 6 added lines, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -86,6 +86,11 @@ if (scalar(@ARGV)==0) {
		print STDOUT "No input file specified, reading from input stream\n";
		}

		# Remove parenthesis
		$ligation_junction =~ s/\(//;
		$ligation_junction =~ s/\)//;

		# with OR \| symbol, this won't work, need to explicitly fix
		my $dangling_junction = substr $ligation_junction, length($ligation_junction)/2;

		# Global variables for calculating statistics
		@@ -261,7 +266,7 @@ while (<>) {
		}
		}
		# read pair contains ligation junction
		if ($record[10] =~ m/$ligation_junction/ \|\| $record[13] =~ m/$ligation_junction/) {
		if ($record[10] =~ m/($ligation_junction)/ \|\| $record[13] =~ m/($ligation_junction)/) {
		$ligation++;
		}
		}