5f856345200f8861b168c85d45e267010d6b55e4
chmalee
  Mon Aug 3 16:40:33 2020 -0700
Update LOVD to bigBed, refs #25841

diff --git src/hg/utils/otto/lovd/download.sh src/hg/utils/otto/lovd/download.sh
index 14c6be7..3cf401a 100755
--- src/hg/utils/otto/lovd/download.sh
+++ src/hg/utils/otto/lovd/download.sh
@@ -1,29 +1,29 @@
 #!/bin/sh -e
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/lovd/check.sh
 #	This script is used via a cron job 
 
 #	cron jobs need to ensure this is true
 umask 002
 
 WORKDIR="/hive/data/outside/otto/lovd"
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in lovd release, Can not find the directory: ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 today=`date +%F`
 mkdir -p $today
 cd $today
 
 # http request needs to come from hgwdev IP address otherwise file not found error
 for db in hg38 hg19
 do
-    wget -q 'http://varcache.lovd.nl/bed/'${db}'?add_id_ncbi=1&add_annotation=1' -O - | grep -v track | grep -v ^$ > lovd.${db}.bed
-    sed -i s/^/chr/g lovd.${db}.bed
-    sed -i 's/effect:/Variant Effect: /g' lovd.${db}.bed
-    sed -i 's/;lovd_count:/<br>Number of LOVD Installations reporting this variant: /g' lovd.${db}.bed
+    wget -q 'http://varcache.lovd.nl/bed/'${db}'?add_id_ncbi=1&add_annotation=1' -O - | \
+        grep -v track | grep -v ^$ | sed -e s/^/chr/g | \
+        tawk '{gsub(";",FS,$6); gsub("effect:|lovd_count:","",$6); print }' | \
+        sort -k1,1 -k2,2n > lovd.${db}.bed
 done