From 4564c508205996e189ab8c4c65d9b2b928da6ae3 Mon Sep 17 00:00:00 2001
From: wbaopaul <yuw1@email.chop.edu>
Date: Sat, 30 Apr 2022 23:30:53 -0400
Subject: [PATCH] enable filter peak by qvalue in integrate module

---
 scripts/integrate_peak.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/integrate_peak.sh b/scripts/integrate_peak.sh
index c973f7a..91de2b3 100755
--- a/scripts/integrate_peak.sh
+++ b/scripts/integrate_peak.sh
@@ -35,11 +35,13 @@ ABS_PATH=`cd "$OUTPUT_DIR"; pwd`
 ## reconstruct the peak-cell matrix
 ## not re-call cells
 mtx_files='TMP' 
+re='^[0-9]+([.][0-9]+)?$'
 for pk0 in "${peaks[@]}"
 do 
-    if [ "$pk0" -eq "$pk0"  ] 2>/dev/null;then
-        continue  ## the gap parameter
+    if [[ $pk0 =~ $re  ]] 2>/dev/null;then
+        continue  ## the gap and qvalue parameter
     fi
+    echo "Reconstruct matrix for sample related to $pk0: "
     sample0=$(basename $pk0)
     sample0=`echo $sample0 | awk -F. '{print $1}'`
     sample0=${sample0/_features_BlacklistRemoved/}