From 8d379f28f636139acaa156c3effec0805e67b8ea Mon Sep 17 00:00:00 2001
From: Bruno Costa <netbofia@hotmail.com>
Date: Mon, 15 Oct 2018 00:50:21 +0100
Subject: [PATCH] Changes counts_merge to use sequenceFilter in invert mode

---
 counts_merge.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/counts_merge.sh b/counts_merge.sh
index a90ec38..ff24f8d 100755
--- a/counts_merge.sh
+++ b/counts_merge.sh
@@ -91,11 +91,11 @@ awk '{print $1}' $novelTasi > $novelTasiSeq
 
 ###Save novel only - No tasi
 head -1  $cons > $novel 
-grep -vwf $tasiTmpSeq $novelTmp | cat >> $novel
+${SCRIPTS_DIR}/sequenceFilter.py -v -s $tasiTmpSeq -d $novelTmp | cat >> $novel
 awk '{if(NR>1){print $1}}' $novel > $novelSeq
 
 ###Save tasi only - Remove novel and conserved reads
-grep -vwf $novelTasiSeq $tasiTmp | grep -vwf $consSeq | cat > $tasi
+${SCRIPTS_DIR}/sequenceFilter.py -v -s $novelTasiSeq -d $tasiTmp | grep -vwf $consSeq | cat > $tasi
 awk '{if(NR>1){print $1}}' $tasi > $tasiSeq