fragstr tag different for single end rt:A:7 so that they are separated within... (a65e8980) · Commits · Chaos / chaos.juicer

SLURM/scripts/chimeric_sam.awk

+1 −1

Changes for SLURM/scripts/chimeric_sam.awk: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -658,7 +658,7 @@ $0 !~ /^@/{
		# get 3' end for second end for dedupping
		interiorpos1 = adjust(pos[0],str[0],cigarstr[0],0);
		sortpos=sprintf("%0" chrlen "d_%0" chrlen "d",pos[0],interiorpos1);
		cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_1_"str[0]"_"str[0]"_"sortpos;
		cb_str = "cb:Z:"chr[0]"_"chr[0]"_0_2_"str[0]"_"str[0]"_"sortpos;
		# read type 7 is singleton reads
		print c[1],"rt:A:7",cb_str;
		}