ea85b03d619559dd267cc8765ca8810d9e706ccd
angie
  Wed Aug 14 14:48:45 2019 -0700
Added instructions for building new altsAndFixes file for gfServer -perSeqMax.  refs #23112

diff --git src/hg/makeDb/doc/hg19.patchUpdate.13.txt src/hg/makeDb/doc/hg19.patchUpdate.13.txt
index 6a43424..4b95f0a 100644
--- src/hg/makeDb/doc/hg19.patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg19.patchUpdate.13.txt
@@ -205,30 +205,42 @@
     ln -sf /hive/data/genomes/hg19/chrom.sizes.initial initial/hg19.chrom.sizes
     ln -sf /hive/data/genomes/hg19/bed/repeatMasker/hg19.fa.align.gz initial/hg19.fa.align.gz
     # Replace top-level files with links to initial/ files
     ln -sf initial/* .
     # End of first-update-only stuff
 
     ln -s /hive/data/genomes/hg19/goldenPath/bigZips/{initial,p13} \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/
 #TODO
     # 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
+
+
+#############################################################################
 # 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)
 # REDONE (except for first-update-only mv) 2018-09-28
     mkdir /hive/data/genomes/hg19/bed/idKeys.p13
     cd /hive/data/genomes/hg19/bed/idKeys.p13