705126cb1d2946056b9da0397acaf2bb6703c6e4
galt
  Tue Oct 12 22:43:02 2021 -0700
finishing off GRC incident step now that QA has pushed hg38.2bit to RR. refs #25091

diff --git src/hg/makeDb/doc/hg38/patchUpdate.13.txt src/hg/makeDb/doc/hg38/patchUpdate.13.txt
index c238378..b3379c0 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.13.txt
@@ -492,35 +492,36 @@
   ok="OK"
   if [ "$c0" -ne "$c1" ]; then
      ok="ERROR"
   fi
   printf "# checking $t: $c0 =? $c1 $ok\n"
 done
 # checking refseq: 639 =? 639 OK
 # checking genbank: 640 =? 640 OK
 # checking assembly: 640 =? 640 OK
     # Note how there's one fewer refseq, consistent with featureBits above.
 
     hgLoadSqlTab hg38 chromAlias $HOME/kent/src/hg/lib/chromAlias.sql ${db}.chromAlias.tab
 
 
 ##############################################################################
-# UCSC to Ensembl (TODO 2021-09-18 galt)
+# UCSC to Ensembl (DONE 2021-09-18 galt)
 # Ask Hiram to update ensembleToUcsc and ensemblLift tables.
 # FYI ensemblLift offset shows how many Ns were inserted by Ensembl to give the right coordinate to alts and fixes.
 #
-
+I asked Hiram to update them and he did.
+However, some questions remain about how best to handle the 57 reversed sequences found on Ensembl chroms.
 
 ############################################################################
 # altLocations and patchLocations (DONE 2021-08-27 galt)
     # indicate corresponding locations between haplotypes and reference
     mkdir /hive/data/genomes/hg38/bed/altLocations.p13
     cd /hive/data/genomes/hg38/bed/altLocations.p13
     ~/kent/src/hg/utils/automation/altScaffoldPlacementToBed.pl \
       /hive/data/genomes/grcH38P13/genbank/GCA_000001405.28_GRCh38.p13_assembly_structure/{ALT_*,PATCHES}/alt_scaffolds/alt_scaffold_placement.txt \
     | sort -k1,1 -k2n,2n \
       > altAndFixLocations.bed
     wc -l altAndFixLocations.bed
 #892 altAndFixLocations.bed
     grep _alt altAndFixLocations.bed > altLocations.bed
     grep _fix altAndFixLocations.bed > fixLocations.bed
     hgLoadBed hg38 altLocations{,.bed}
@@ -870,24 +871,24 @@
 
 ##############################################################################
 # OMIM tracks (TODO - 2020-? angie)
 # the otto process builds the omim* tables; edit otto/omim/buildOmimTracks.sh to make sure
 # the most recent dbSNP version is listed for the db.  After the snpNNN table is updated to
 # include patch sequences, the next otto update will include patches.
 # omimGene2 is still using refGene, but I think it would be better if it used ncbiRefSeqCurated
 # if it exists.
 
 # TODO: OMIM Genes needs liftOver to new alts and fixes (or redo from ncbiRefSeq).
 # OMIM Phenotypes needs liftOvers to all alts and fixes.  Sometimes it spans a region larger
 # than an alt/fix, so maybe lower the percentage that has to map?
 
 
 ##############################################################################
-# GRC Incident Database (TODO 2021-? galt)
+# GRC Incident Database (DONE 2021-10-12 galt)
 
     # Wait until the updated hg38 files have been pushed to RR because GRC Incident update is
     # automated.  Then update the file used to map GRC's RefSeq accessions to our names:
     hgsql hg38 -NBe 'select alias,chrom from chromAlias where source = "refseq" order by alias;' \
       > /hive/data/outside/grc/incidentDb/GRCh38/refSeq.chromNames.tab
 
 
 #############################################################################