8cf5d04b02f2bacf4fb496891d9cfc3cd99e8df8
hiram
  Tue Feb 20 10:33:36 2024 -0800
recover from otto update refs #32902

diff --git src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
index e022ea6..eca9fea 100644
--- src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
+++ src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
@@ -20,30 +20,33 @@
 ~/kent/src/hg/makeDb/doc/mm39/gffToLink.pl > to.add.ncbiRefSeqLink.tsv
 
 # obtain the genePred file from the genomic.gff.gz file:
 
 export asmId=GCF_000001635.27_GRCm39
 export downloadDir=/hive/data/genomes/mm39/bed/ncbiRefSeq.2023-04-19/download
 export ncbiGffGz=$downloadDir/${asmId}_genomic.gff.gz
 
 zcat $ncbiGffGz \
     | sed -re 's/([;\t])SO_type=/\1so_type=/;' \
       | gff3ToGenePred  -refseqHacks -attrsOut=$asmId.attrs.txt \
         -unprocessedRootsOut=$asmId.unprocessedRoots.txt stdin raw.$asmId.gp
 
 grep NC_005089.1 raw.$asmId.gp > NC_005089.1.gp
 sed -e 's/NC_005089.1/chrM/g;' NC_005089.1.gp > chrM.gp
+hgLoadGenePred -genePredExt mm39 chrMRefSeq chrM.gp
+hgsql -N -e 'select * from chrMRefSeq;' mm39 > to.add.chrM.sql.tsv
+hgsql -e 'drop table chrMRefSeq;' mm39
 
 # save the existing files in case they are broken during this process:
 hgsql -N -e 'select * from ncbiRefSeq;' mm39 > before.mm39.ncbiRefSeq.tsv
 hgsql -N -e 'select * from ncbiRefSeqCurated;' mm39 > before.mm39.ncbiRefSeqCurated.tsv
 hgsql -N -e 'select * from ncbiRefSeqLink;' mm39 > before.mm39.ncbiRefSeqLink.tsv
 
 # loading the genePred data into two tables:
 
 hgsql -N -e 'select count(*) from ncbiRefSeq;' mm39
 # 134700
 hgsql -e 'LOAD DATA LOCAL INFILE "to.add.chrM.sql.tsv" INTO TABLE ncbiRefSeq;' mm39
 hgsql -N -e 'select count(*) from ncbiRefSeq;' mm39
 # 134737
 
 hgsql -N -e 'select count(*) from ncbiRefSeqCurated;' mm39