12e803e0ba9fd1b68163960b8b8e2bc876558b28
chmalee
  Fri Aug 14 14:29:20 2020 -0700
When switching LOVD to bigBed, I overwrote the message to check chrMT instead of chrM for annotations, good find by Angie, refs #26021

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index 718c221..925ca02 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -1,64 +1,66 @@
 #!/bin/sh -e
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/otto/lovd/check.sh
 #	This script is used via a cron job 
 
 umask 002
 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
 new38Cc=`cat lovd.hg38.bed | $TAWK '(NF!=7)' | wc -l`
 new19Cc=`cat lovd.hg19.bed | $TAWK '(NF!=7)' | wc -l`
 if [ "$new38Cc" -ne "0" ]; then
         echo LVOD hg38 $today: found rows with not six columns, quitting
         exit 255
 fi
 if [ "$new19Cc" -ne "0" ]; then
         echo LVOD hg19 $today: found rows with not six columns, quitting
         exit 255
 fi
 
 for db in hg38 hg19
 do
     if [ ${db} == "hg19" ]
     then
         $KENTBIN/bedClip lovd.${db}.bed /cluster/data/${db}/chrom.sizes stdout | sed -e 's/^chrM/chrMT/g' > lovd.${db}.clipped.bed
     else
         $KENTBIN/bedClip lovd.${db}.bed /cluster/data/${db}/chrom.sizes lovd.${db}.clipped.bed
     fi
 
+    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)<50)' > lovd.${db}.short.bed
+    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)>=50)' > lovd.${db}.long.bed
     if [ ${db} == "hg19" ]
     then
         echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t\t' >> lovd.${db}.short.bed
         echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t\t' >> lovd.${db}.long.bed
     fi
-    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)<50)' > lovd.${db}.short.bed
-    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)>=50)' > lovd.${db}.long.bed
 
+    sort -k1,1 -k2,2n lovd.${db}.short.bed > lovd.${db}.short.bed.sorted
+    sort -k1,1 -k2,2n lovd.${db}.long.bed > lovd.${db}.long.bed.sorted
     oldShortLc=`bigBedToBed ../release/${db}/lovd.${db}.short.bb stdout | wc -l`
     oldLongLc=`bigBedToBed ../release/${db}/lovd.${db}.long.bb stdout | wc -l`
-    newShortLc=`wc -l lovd.${db}.short.bed | cut -d' ' -f1`
-    newLongLc=`wc -l lovd.${db}.long.bed | cut -d' ' -f1`
+    newShortLc=`wc -l lovd.${db}.short.bed.sorted | cut -d' ' -f1`
+    newLongLc=`wc -l lovd.${db}.long.bed.sorted | cut -d' ' -f1`
     echo ${db} short rowcount: old $oldShortLc new: $newShortLc
     echo ${db} long rowcount: old $oldLongLc new: $newLongLc
     echo $oldShortLc $newShortLc | awk -v d=${db} '{if (($2-$1)/$1 > 0.1) {printf "validate on %s LOVD short failed: old count: %d, new count: %d\n", d,$1,$2; exit 1;}}'
     echo $oldLongLc $newLongLc | awk -v d=${db} '{if (($2-$1)/$1 > 0.1) {printf "validate on %s LOVD long failed: old count: %d, new count: %d\n", d,$1,$2; exit 1;}}'
 
-    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.short.bed /cluster/data/${db}/chrom.sizes lovd.${db}.short.bb
-    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.long.bed /cluster/data/${db}/chrom.sizes lovd.${db}.long.bb
+    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.short.bed.sorted /cluster/data/${db}/chrom.sizes lovd.${db}.short.bb
+    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.long.bed.sorted /cluster/data/${db}/chrom.sizes lovd.${db}.long.bb
     mkdir -p ${WORKDIR}/release/${db}
     cp lovd.${db}.{short,long}.bb ${WORKDIR}/release/${db}/
 done
 
 echo LOVD update: OK