ee4c78e5d1d630be90e7ca6bc0c076fa0ffd3464
galt
  Wed Feb 1 16:07:41 2023 -0800
minor makedoc update for final hg38 p14 patch.

diff --git src/hg/makeDb/doc/hg38/patchUpdate.14.txt src/hg/makeDb/doc/hg38/patchUpdate.14.txt
index 5a923fd..1326124 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.14.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.14.txt
@@ -883,52 +883,53 @@
 echo "    <TR><TD><FONT SIZE=-1>chromosomes</FONT></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$numChroms</FONT></TD></TR>"
 set numHaps = ( `hgsql $db -BN -e "select count(*) from chromInfo where chrom like '%\_alt'"` )
 echo "    <TR><TD><FONT SIZE=-1>haplotypes</FONT></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$numHaps</FONT></TD></TR>"
 set numFixes = ( `hgsql $db -BN -e "select count(*) from chromInfo where chrom like '%\_fix'"` )
 echo "    <TR><TD><FONT SIZE=-1>fixes</FONT></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$numFixes</FONT></TD></TR>"
 set numUnlocal = ( `hgsql $db -BN -e "select count(*) from chromInfo where chrom like '%\_random'"` )
 echo "    <TR><TD><FONT SIZE=-1>unlocalized contigs</FONT></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$numUnlocal</FONT></TD></TR>"
 set numChrUns = ( `hgsql $db -BN -e "select count(*) from chromInfo where chrom like '%chrUn\_%'"` )
 echo "    <TR><TD><FONT SIZE=-1>unplaced contigs</FONT></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$numChrUns</FONT></TD></TR>"
 echo "    <TR><TD></TD><TD></TD></TR>"
 @ totalChroms = ($numChroms + $numHaps + $numFixes + $numUnlocal + $numChrUns)
 echo "    <TR><TD><B><FONT SIZE=-1>Total</FONT></B></TD><TD ALIGN=\"CENTER\"><FONT SIZE=-1>$totalChroms</FONT></TD></TR>"
 echo "</TABLE>"
 echo "</p>"
 
-
+FYI I had to manually reorder some rows in the stats table so they were in a readable order instead in alphabetical order by chrom name,
+but it was quite eay to do with vim.
 
 
 #############################################################################
 # DBSNP V156 (TODO - 2022-11-17 Galt)
 #
 # We have to wait for at least v156 to get African study data H3AFRICA.
 # I did dbsnp for v155.  See the bigDbSnp.txt makedoc.
 
 ##############################################################################
 # OMIM tracks (TODO - 2022-11-? Galt)
 # 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?
 
 # Are any of the otto's using 
 /hive/data/genomes/hg38/jkStuff/hg38.p13.alt.psl
 and should they get changed to the new one?
 /hive/data/genomes/hg38/jkStuff/hg38.p14.alt.psl
 
 
 ##############################################################################
-# GRC Incident Database (TODO 2021-10-12 galt)
+# GRC Incident Database (DONE 2023-01-31 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
 
 
 #############################################################################