557555a3b5289cbb7d7c75c5b4ab423bfe35fc1c
angie
  Mon Feb 24 16:35:45 2020 -0800
Build hg19.altsAndFixes.p13.plusMT (and document the /hive/data/genomes/$db/altsAndFixes symlink).  refs #24648

diff --git src/hg/makeDb/doc/hg19.patchUpdate.13.txt src/hg/makeDb/doc/hg19.patchUpdate.13.txt
index b5fd706..5ba0d38 100644
--- src/hg/makeDb/doc/hg19.patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg19.patchUpdate.13.txt
@@ -225,30 +225,32 @@
     # Edit README.txt
 
     # TODO: /hive/data/genomes/hg19/goldenPath/chromosomes/
 
 
 #############################################################################
 # Build perSeqMax file for gfServer (hgBlat) (DONE 19-08-14 angie)
     # When the blat server is restarted with the updated hg19.2bit file,
     # hg19.altsAndFixes needs to be copied over along with the new hg19.2bit file,
     # and gfServer needs to be restarted with -perSeqMax=hg19.altsAndFixes.
     cd /hive/data/genomes/hg19
     cut -f 1 chrom.sizes.p13 \
     | grep -E '_(alt|fix|hap.*)$' \
     | sed -re 's/^/hg19.2bit:/;' \
       > hg19.altsAndFixes.p13
+    # Link for blat server installation convenience:
+    ln -sf hg19.altsAndFixes.p13 altsAndFixes
 
 
 #############################################################################
 # Extend cytoBandIdeo (DONE 2018-09-28 angie)
 # UNDONE 2018-09-28 (see ROLL IT ALL BACK below)
 # REDONE 2018-09-28
     cd /hive/data/genomes/hg19/bed/cytoBand
     tawk '{print $1, 0, $2, "", "gneg";}' /hive/data/genomes/grcH37P13/chrom.sizes \
       > cytoBand.p13.tab
     hgLoadSqlTab -oldTable hg19 cytoBandIdeo - cytoBand.p13.tab
 
 
 #########################################################################
 # Regenerate idKeys with extended hg19 (DONE - 2018-09-28 - Angie)
 # UNDONE 2018-09-28 (see ROLL IT ALL BACK below)