b98ba30fa69bf7ff12c58db12776589373e24e95
max
  Mon Nov 4 05:04:51 2019 -0800
splitting lovd track into composite with two subtracks, refs #24408

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index 740b02f..7440d28 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -7,51 +7,54 @@
 WORKDIR="/hive/data/outside/otto/lovd"
 TAWK=/cluster/bin/scripts/tawk
 KENTBIN=/cluster/bin/x86_64/
 
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in lovd release, Can not find the directory: ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 today=`date +%F`
 cd $today
 
 # count columns and make sure new files have 6 columns
 new19Cc=`cat lovd.hg19.bed | $TAWK '(NF!=6)' | wc -l`
-new18Cc=`cat lovd.hg18.bed | $TAWK '(NF!=6)' | wc -l`
+#new18Cc=`cat lovd.hg18.bed | $TAWK '(NF!=6)' | wc -l`
 if [ "$new19Cc" -ne "0" ]; then
         echo LVOD hg19 $today: found rows with not six columns, quitting
         exit 255
 fi
-if [ "$new18Cc" -ne "0" ]; then
-        echo LVOD hg18 $today: found rows with not six columns, quitting
-        exit 255
-fi
+
+#if [ "$new18Cc" -ne "0" ]; then
+#        echo LVOD hg18 $today: found rows with not six columns, quitting
+#        exit 255
+#fi
 
 # compare old and new line counts and abort if no increase
 old19Lc=`$KENTBIN/hgsql hg19 -e "SELECT COUNT(*) from lovd" -NB`
 new19Lc=`wc -l lovd.hg19.bed | cut -d' ' -f1 `
-old18Lc=`$KENTBIN/hgsql hg18 -e "SELECT COUNT(*) from lovd" -NB`
-new18Lc=`wc -l lovd.hg18.bed | cut -d' ' -f1 `
+#old18Lc=`$KENTBIN/hgsql hg18 -e "SELECT COUNT(*) from lovd" -NB`
+#new18Lc=`wc -l lovd.hg18.bed | cut -d' ' -f1 `
 
 echo hg19 rowcount: old $old19Lc new: $new19Lc
-echo hg18 rowcount: old $old18Lc new: $new18Lc
+#echo hg18 rowcount: old $old18Lc new: $new18Lc
 
 if [ "$new19Lc" -eq "$old19Lc" ]; then
         echo LVOD hg19: rowcount for $today is equal to old rowcount in mysql, quitting
         exit 0
 fi
 
 # commenting out, as LOVD count will go down in the future, because they have a 
 # db cleanup procedure in place now
-#if [ "$new19Lc" -lt "$old19Lc" ]; then
-        #echo LVOD hg19: rowcount for $today is smaller to old rowcount in mysql, quitting
-        #exit 255
-#fi
+if [ "$new19Lc" -lt "$old19Lc" ]; then
+        echo LOVD hg19: rowcount for $today is smaller to old rowcount in mysql, quitting
+        exit 255
+fi
 
 # bedDetail4.sql was generated like this:
 # egrep -v 'score|strand|thick|reserved|block|chromStarts' /cluster/home/max/kent/src/hg/lib/bedDetail.sql > bedDetail4.sql 
 # need to use bedClip as current files include invalid coords which LOVD won't fix.
-$KENTBIN/bedClip lovd.hg19.bed /cluster/data/hg19/chrom.sizes stdout | $KENTBIN/hgLoadBed hg19 lovd stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-$KENTBIN/bedClip lovd.hg18.bed /cluster/data/hg18/chrom.sizes stdout | $KENTBIN/hgLoadBed hg18 lovd stdin  -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
+$KENTBIN/bedClip lovd.hg19.bed /cluster/data/hg19/chrom.sizes lovd.hg19.clipped.bed
+cat lovd.hg19.clipped.bed | awk '(($3-$2)<=100)' | $KENTBIN/hgLoadBed hg19 lovdShort stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
+cat lovd.hg19.clipped.bed | awk '(($3-$2)>100)' | $KENTBIN/hgLoadBed hg19 lovdLong stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
+#$KENTBIN/bedClip lovd.hg18.bed /cluster/data/hg18/chrom.sizes stdout | $KENTBIN/hgLoadBed hg18 lovd stdin  -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin