2aa7e21e10d367a62a09e29db5f9f3703e210012
angie
  Wed Aug 14 14:54:11 2019 -0700
Slight tweak to altsAndFixes: don't forget to add patch version.  refs #23112

diff --git src/hg/makeDb/doc/hg38/patchUpdate.12.txt src/hg/makeDb/doc/hg38/patchUpdate.12.txt
index 1868fab..2a789c6 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.12.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.12.txt
@@ -170,31 +170,31 @@
     ln -sf /hive/data/genomes/hg38/chrom.sizes \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest/hg38.chrom.sizes
     ln -sf /hive/data/genomes/hg38/chrom.sizes.p12 \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p12/hg38.p12.chrom.sizes
 
 
 #############################################################################
 # Build perSeqMax file for gfServer (hgBlat) (DONE 19-08-14 angie)
     # When the blat server is restarted with the updated hg38.2bit file,
     # hg38.altsAndFixes needs to be copied over along with the new hg38.2bit file,
     # and gfServer needs to be restarted with -perSeqMax=hg38.altsAndFixes.
     cd /hive/data/genomes/hg38
     cut -f 1 chrom.sizes.p12 \
     | grep -E '_(alt|fix)$' \
     | sed -re 's/^/hg38.2bit:/;' \
-      > hg38.altsAndFixes
+      > hg38.altsAndFixes.p12
 
 
 #########################################################################
 # Regenerate idKeys with extended hg38 (DONE - 2018-08-10 - Angie)
 
     mkdir /hive/data/genomes/hg38/bed/idKeys.p12
     cd /hive/data/genomes/hg38/bed/idKeys.p12
     # ku down... use hgwdev this time:
     time ($HOME/kent/src/hg/utils/automation/doIdKeys.pl \
       -twoBit=/hive/data/genomes/hg38/hg38.p12.unmasked.2bit \
       -bigClusterHub=hgwdev -smallClusterHub=hgwdev \
         -buildDir=`pwd` hg38) > do.log 2>&1 &
     tail -f do.log
 #real    1m21.903s
     cat hg38.keySignature.txt