From cc83af09b8bda1e0b4a6d5589486431c30bfc745 Mon Sep 17 00:00:00 2001
From: Bob Harris <rsharris@bx.psu.edu>
Date: Tue, 3 Apr 2018 19:38:48 -0400
Subject: [PATCH] corrected the improper use of uninitialized sabutan
 environemnt variable

---
 scripts/order_query_results.sh            | 2 +-
 scripts/order_query_results_workaround.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/order_query_results.sh b/scripts/order_query_results.sh
index 8108bc9..7cba752 100755
--- a/scripts/order_query_results.sh
+++ b/scripts/order_query_results.sh
@@ -55,7 +55,7 @@ cat temp.${sabutanOutput}.leaf_to_queries \
       #
       cat ${queryFiles} \
         | python ${thisScriptDir}/pluck_from_fasta.py --sequences=${queries} \
-        | ${sabutan} query \
+        | sabutan query \
           --tree=temp.${sabutanOutput}.${leaf}.sbt --threshold=${specificity} \
           --countallkmerhits \
         | awk '/^[*]/  { }
diff --git a/scripts/order_query_results_workaround.sh b/scripts/order_query_results_workaround.sh
index f7c718f..c3ce52c 100755
--- a/scripts/order_query_results_workaround.sh
+++ b/scripts/order_query_results_workaround.sh
@@ -57,7 +57,7 @@ cat temp.${tempFileId}.leaf_to_queries \
       #
       cat ${queryFiles} \
         | python ${thisScriptDir}/pluck_from_fasta.py --sequences=${queries} \
-        | ${sabutan} query \
+        | sabutan query \
           --tree=temp.${tempFileId}.${leaf}.sbt --threshold=${specificity} \
           --countallkmerhits \
         | awk '/^[*]/  { }