fixed small bug in chimeric script, added alignonly mode to juicer (4096a0a7) · Commits · Chaos / chaos.juicer

CPU/common/chimeric_blacklist.awk

+3 −3

Original line number	Diff line number	Diff line
		@@ -119,6 +119,7 @@ $0 !~ /^@/{
		mapped[j] = and(tmp[2],4) == 0;
		sum_mapped = sum_mapped+mapped[j];
		}

		if (sum_mapped < 2) {
		# unmapped
		for (j=1; j <= count; j++) {
		@@ -378,7 +379,6 @@ END{
		# (chimeric pair, depends on where the ends are)
		# 4 will be chimeric paired or abnormal
		# (chimeric pair, depends on where the ends are)
		sum_mapped=0;
		for (j=1; j <= count; j++) {
		split(c[j], tmp);
		# first in pair: 64

+7 −1

Original line number	Diff line number	Diff line
		@@ -146,6 +146,7 @@ then
		early) earlyexit=1 ;;
		final) final=1 ;;
		postproc) postproc=1 ;;
		alignonly) alignonly=1 ;;
		*) echo "$usageHelp"
		echo "$stageHelp"
		exit 1
		@@ -424,6 +425,11 @@ then
		done
		fi

		if [ -n "$alignonly" ]
		then
		exit 0
		fi

		#MERGE SORTED AND ALIGNED FILES
		if [ -z $final ] && [ -z $dedup ] && [ -z $postproc ]
		then