From b40af9e73b3c69e8a15ad62ff04ad9ca768c3a12 Mon Sep 17 00:00:00 2001
From: JustinChu <justinchu1989@gmail.com>
Date: Wed, 21 Mar 2018 19:16:14 -0700
Subject: [PATCH] fix -p and -B options

---
 bin/kollector_multiple.sh | 28 ++++++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/bin/kollector_multiple.sh b/bin/kollector_multiple.sh
index 12c0c3a..9f53458 100755
--- a/bin/kollector_multiple.sh
+++ b/bin/kollector_multiple.sh
@@ -121,9 +121,19 @@ then
 	cd iteration.$i
 	if [ -z ${p+x} ]
 	then
-	kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -n$n -o$o -B$B ../$seed_symlink $pet1 $pet2
+		if [ -z ${B+x} ]
+		then
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -n$n -o$o -B$B ../$seed_symlink $pet1 $pet2
+		else
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -n$n -o$o ../$seed_symlink $pet1 $pet2
+		fi
 	else
-	kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -p$p -n$n -o$o -B$B ../$seed_symlink $pet1 $pet2
+		if [ -z ${B+x} ]
+		then
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -p$p -n$n -o$o -B$B ../$seed_symlink $pet1 $pet2
+		else
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -p$p -n$n -o$o ../$seed_symlink $pet1 $pet2
+		fi
 	fi
 	cut -f2 -d " " ${o}_hitlist.txt|sort|uniq > ${o}_succeedtranscripts.txt
 	grep ">" ../$seed_symlink | sed 's/>//g' | sed 's/\s.*//g' > ${o}_alltranscripts.txt
@@ -140,9 +150,19 @@ else
 	seed_new="$(pwd)"/${o}_prevfailed.fa
 	if [ -z ${p+x} ]
 	then
-	kollector.sh -j$j -d$d -k$k -K$K -r$newr -s$s -n$n -o$o -B$B $seed_new $pet1 $pet2
+		if [ -z ${B+x} ]
+		then
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -n$n -o$o -B$B $seed_new $pet1 $pet2
+		else
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -n$n -o$o $seed_new $pet1 $pet2
+		fi
 	else
-	kollector.sh -j$j -d$d -k$k -K$K -r$newr -s$s -p$p -n$n -o$o -B$B $seed_new $pet1 $pet2
+		if [ -z ${B+x} ]
+		then
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -p$p -n$n -o$o -B$B $seed_new $pet1 $pet2
+		else
+			kollector.sh -j$j -d$d -k$k -K$K -r$r -s$s -p$p -n$n -o$o $seed_new $pet1 $pet2
+		fi
 	fi
 	cut -f2 -d " " ${o}_hitlist.txt|sort|uniq > ${o}_succeedtranscripts.txt
 	grep ">" ${o}_prevfailed.fa | sed 's/>//g' | sed 's/\s.*//g' > ${o}_alltranscripts.txt