0ba0086f3d6f31f631f8496aca509c32dc19951f
chmalee
  Mon Mar 30 13:29:15 2020 -0700
Fix early exit from missing braces in lovd otto script, no refs

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index 4c20d3e..e820bb3 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -53,26 +53,26 @@
 if [ "$new19LongLc" -eq "$old19LongLc" ]; then
         echo LOVD hg19 long: rowcount for $today is equal to old rowcount in mysql, quitting
         exit 0
 fi
 
 if [ "$new19ShortLc" -lt "$old19ShortLc" ]; then
         echo LOVD hg19 short: rowcount for $today is smaller to old rowcount in mysql, quitting
         exit 255
 fi
 
 if [ "$new19LongLc" -lt "$old19LongLc" ]; then
         echo LOVD hg19 long: rowcount for $today is smaller to old rowcount in mysql, quitting
         exit 255
 fi
 
-echo $old19ShortLc $new19ShortLc | awk '{if (($2-$1)/$1 > 0.1) printf "validate on hg19 LOVD short failed: old count: %d, new count: %d\n", $1,$2; exit 1;}'
-echo $old19LongLc $new19LongLc | awk '{if (($2-$1)/$1 > 0.1) printf "validate on hg19 LOVD long failed: old count: %d, new count: %d\n", $1,$2; exit 1;}'
+echo $old19ShortLc $new19ShortLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg19 LOVD short failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
+echo $old19LongLc $new19LongLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg19 LOVD long failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
 
 # 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 lovd.hg19.clipped.bed
 cat lovd.hg19.short.bed | $KENTBIN/hgLoadBed hg19 lovdShort stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
 cat lovd.hg19.long.bed | $KENTBIN/hgLoadBed hg19 lovdLong stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
 #$KENTBIN/bedClip lovd.hg18.bed /cluster/data/hg18/chrom.sizes stdout | $KENTBIN/hgLoadBed hg18 lovd stdin  -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
 echo LOVD update: OK