282d648d8896a7bb45af20bbc306873f6a5ffb87
angie
  Wed Jan 17 11:03:32 2024 -0800
Added chrUn_KI270752v1 to hg38.{p11,p12,p13}.chromAlias.txt files after user pointed out in MLQ #32874 that it was missing.
It is present in hg38.p14.chromAlias.txt and all *chromAlias.bb files.

diff --git src/hg/makeDb/doc/hg38/patchUpdate.13.txt src/hg/makeDb/doc/hg38/patchUpdate.13.txt
index b3379c0..65d7a18 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.13.txt
@@ -880,15 +880,36 @@
 # 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 (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
 
 
 #############################################################################
+# Update hg38.p13.chromAlias.txt (DONE 2024-01-17 Angie)
+
+    # In MLQ#32874, the user reported that chrUn_KI270752v1 is missing from hg38.p12.chromAlias.txt.
+    # That's because when the hg38.{p11,p12,p13}.chromAlias.txt files were initially created
+    # above ("Correctly versioned hg38.chromAlias.txt files in downloads"),
+    # chrUn_KI270752v1 was omitted because it had been removed from the RefSeq assembly as
+    # contamination.  However, it is confusing for users to have a sequence in the db with no
+    # aliases despite it having Assembly, Ensembl and INSDC aliases.  So add it back.
+    hgsql hg38 -NBe 'select * from chromAlias where chrom = "chrUn_KI270752v1"'
+#HSCHRUN_RANDOM_CTG29    chrUn_KI270752v1        assembly
+#KI270752.1      chrUn_KI270752v1        ensembl,genbank
+    cd /hive/data/genomes/hg38/goldenPath/bigZips
+    echo -e "chrUn_KI270752v1\tHSCHRUN_RANDOM_CTG29\tKI270752.1\t" >> hg38.p13.chromAlias.txt
+    # p13/hg38.p13.chromAlias.txt is a symlink to the one in this directory.
+    # p13/hg38.p13.chromAlias.bb is a file in p13/ .  -- But it already has chrUn_KI270752v1
+    # so it does not need to be updated, great.
+    bigBedToBed -chrom=chrUn_KI270752v1 p13/hg38.p13.chromAlias.bb stdout
+#chrUn_KI270752v1        0       27745   chrUn_KI270752v1        HSCHRUN_RANDOM_CTG29    KI270752.1      KI270752.1
+
+
+#############################################################################