From 6d3da40f7879f3076b7cc68d662962fcea80cf28 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= <jens.preussner@mpi-bn.mpg.de>
Date: Wed, 28 Oct 2015 10:21:47 +0100
Subject: [PATCH] Defused a potential breaking for loop on unfixed number of
 files

---
 src/admire | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/admire b/src/admire
index b13a316..0c5137e 100755
--- a/src/admire
+++ b/src/admire
@@ -466,7 +466,8 @@ print id,name,gid,type,$1,$2,$3,$6,$7,$8,$9,$10,higherin,qval,$14,$11,$12,$13;}'
 			fi
 			sort -t',' -k14,14n $EXCEL/$g-$r.csv | cut -d',' -f5,6,7 | sed -e 's/,/\t/g' | tail -n +2 | head -n $I > $VISUALIZATION/$g/$r-target.bed
 			split -l 1 $VISUALIZATION/$g/$r-target.bed $VISUALIZATION/$g/$r-target-
-			for f in $VISUALIZATION/$g/$r-target-*; do
+			targets = $(ls $VISUALIZATION/$g/$r-target-*)
+			for f in $targets; do
 				bedtools intersect -wa -a $DIR/../data/ilmn12.hg19.bed -b $f | awk 'BEGIN{FS="\t";OFS="\t";}{split($4,a,";");split(a[1],b,"=");print b[2],$2}' | sort > $f.probes
 				cut -f1 $f.probes | grep -f - $WORKDIR/normalized/betaValues_fn.sorted.txt > $f.grep
 				cut -f2 $f.probes | paste - $f.grep > $f.txt