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.11.txt src/hg/makeDb/doc/hg38/patchUpdate.11.txt
index 28285ff..028c090 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.11.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.11.txt
@@ -685,16 +685,37 @@
               /hive/data/genomes/hg38/chrom.sizes \
               {check out exists $track.plusP11.bw}
     done < wgEncodeRegDnaseWig.gbdbToOrigFile.tab > jobList
     para make jobList
     para time
 #Completed: 95 of 95 jobs
 #CPU time in finished jobs:     136582s    2276.37m    37.94h    1.58d  0.004 y
 #IO & Wait Time:                     0s       0.00m     0.00h    0.00d  0.000 y
 #Average job time:                 463s       7.72m     0.13h    0.01d
 #Longest finished job:             884s      14.73m     0.25h    0.01d
 #Submission to last job:          1684s      28.07m     0.47h    0.02d
 
     # Don't update /gbdb -- use .plusP11 files to make .plusP12.
 
 
+#############################################################################
+# Update hg38.p11.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
+    # in patchUpdate.13.txt ("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.p11.chromAlias.txt
+    # p11/hg38.p11.chromAlias.txt is a symlink to the one in this directory.
+    # p11/hg38.p11.chromAlias.bb is a file in p11/ .  -- But it already has chrUn_KI270752v1
+    # so it does not need to be updated, great.
+    bigBedToBed -chrom=chrUn_KI270752v1 p11/hg38.p11.chromAlias.bb stdout
+#chrUn_KI270752v1        0       27745   chrUn_KI270752v1        HSCHRUN_RANDOM_CTG29    KI270752.1      KI270752.1
+
+
 ##############################################################################