4deb0c9ffddc09de17d71a387cec95c9a1cbfc14
angie
  Thu Feb 20 11:30:48 2020 -0800
Oops, need to ensure sortedness of db tables after adding patch sequences - thx Jairo.  refs #24648

diff --git src/hg/makeDb/doc/hg38/patchUpdate.12.txt src/hg/makeDb/doc/hg38/patchUpdate.12.txt
index 2a789c6..2c015c1 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.12.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.12.txt
@@ -32,30 +32,35 @@
     ln -sf chrom.sizes.p12 chrom.sizes
 
     cd /hive/data/genomes/hg38/bed/chromInfo
     hgLoadSqlTab hg38 chromInfo chromInfo.sql chromInfo.p12.tab
 
 
 ##############################################################################
 # Extend main database tables for fileless tracks (DONE - 2018-08-10 - Angie)
 
     # Just add the patch table rows to the main database tables
     for table in gap gold rmsk simpleRepeat windowmaskerSdust cpgIslandExt genscan augustusGene; do
       echo $table
       hgsql hg38 -e "insert into hg38.$table select * from grcH38P12.$table"
     done
 
+    #*** NOTE for NEXT TIME: check results with positionalTblCheck in case they need to be resorted:
+    for table in gap gold rmsk simpleRepeat windowmaskerSdust cpgIslandExt genscan augustusGene; do
+      positionalTblCheck hg38 $table
+    done
+
 
 ##############################################################################
 # Extend main database gc5BaseBw.bw (DONE - 2018-08-10 - Angie)
 
     cd /hive/data/genomes/hg38/bed/gc5Base/
     # Concatenate original assembly results with grcH38P12 results
     time (zcat hg38.gc5Base.wigVarStep.gz \
         /hive/data/genomes/grcH38P12/bed/gc5Base/grcH38P12.gc5Base.wigVarStep.gz \
       | gzip -c \
       > hg38.p12.gc5Base.wigVarStep.gz)
 #real    8m9.913s
     # Make a new gc5BaseBw.bw
     time wigToBigWig hg38.p12.gc5Base.wigVarStep.gz ../../chrom.sizes.p12 \
       hg38.p12.gc5Base.bw
 #real    16m33.792s