From 456cef353484f7cb1bd460238e3d58554cd02368 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Wed, 12 May 2021 22:46:48 -0400
Subject: [PATCH] update conversion script

---
 scripts/lepmap2anchor | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/lepmap2anchor b/scripts/lepmap2anchor
index 4c85dc5..9a22f0a 100755
--- a/scripts/lepmap2anchor
+++ b/scripts/lepmap2anchor
@@ -12,17 +12,17 @@ EOF
   exit 1
 fi
 
-LG=$(ls intervals/*.intervals | wc -l)
+LG=$(ls 7_Intervals/*.intervals | wc -l)
 
 if [ ! -f $1 ]; then
     echo "Error: marker file $(echo $1) not found. It may be generated using scripts/extract_markers.sh"
     exit 1
 fi
 
-echo "Identified $LG interval files in intervals/ directory"
+echo "Identified $LG interval files in 7_Intervals/ directory"
 
 for i in $(seq 1 $LG); do
-    awk -vn=$i '(NR==FNR){map[NR-1]=$0}(NR!=FNR){$1=map[$1] "\t" n;print}' $1 intervals/ordered.$i.intervals >> lepmap3_intervals.la
+    awk -vn=$i '(NR==FNR){map[NR-1]=$0}(NR!=FNR){$1=map[$1] "\t" n;print}' $1 7_Intervals/ordered.$i.intervals >> lepmap3_intervals.la
 done
 
 echo "Created Lep-Anchor input file lepmap3_intervals.la"