From 07909d22f2ce1a4b9b15206dbb8898586d4c4dfc Mon Sep 17 00:00:00 2001
From: Pierre Peterlongo <pierre.peterlongo@inria.fr>
Date: Mon, 3 Jul 2017 10:37:37 +0200
Subject: [PATCH] src counter now outputs a percentage of positions covered by
 shared kmers from the bank file - .sh fix

---
 short_read_connector.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/short_read_connector.sh b/short_read_connector.sh
index b590c97..76d8f5d 100755
--- a/short_read_connector.sh
+++ b/short_read_connector.sh
@@ -256,9 +256,11 @@ fi
 if [ $diskMode -eq 0 ]; then
     if [ $countMode -eq 0 ]; then
         cmd="${BIN_DIR}/SRC_linker_ram"
+        threshold_option="-kmer_threshold ${kmer_threshold}"
     else
         # SRC_COUNTER
         cmd="${BIN_DIR}/SRC_counter"
+        threshold_option=""
     fi
 else
     echo "Disk version not maintained anymore - sorry"
@@ -274,7 +276,7 @@ fi
 
 
 # adding options
-cmd="${cmd} -graph ${out_dsk}  -bank ${bank_set} -query ${query_set} -out ${result_file} -kmer_threshold ${kmer_threshold} -fingerprint_size ${fingerprint_size} -core ${core_used} -gamma ${gamma} ${commet_like_option} ${zerod_option} ${keep_low_complexity_option}"
+cmd="${cmd} -graph ${out_dsk}  -bank ${bank_set} -query ${query_set} -out ${result_file} ${threshold_option} -fingerprint_size ${fingerprint_size} -core ${core_used} -gamma ${gamma} ${commet_like_option} ${zerod_option} ${keep_low_complexity_option}"