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/hg38/patchUpdate.12.txt src/hg/makeDb/doc/hg38/patchUpdate.12.txt
index f26cac2..1868fab 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.12.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.12.txt
@@ -1,19 +1,19 @@
 # for emacs: -*- mode: sh; -*-
 
 # This file describes how hg38 was extended with patch sequences and annotations from grcH38P12,
-# after having been extended with grcH38P11 (see patchUpdate.11.txt).
+# after having been extended with grcH38P1 (see patchUpdate.11.txt).
 
 ##############################################################################
 # Extend main database 2bit, chrom.sizes, chromInfo (DONE - 2018-08-10 - Angie)
 
     cd /hive/data/genomes/hg38
     # main 2bit
     time faToTwoBit <(twoBitToFa hg38.2bit stdout) \
            <(twoBitToFa /hive/data/genomes/grcH38P12/grcH38P12.2bit stdout) \
            hg38.p12.2bit
 #real    1m33.136s
     # unmasked 2bit
     twoBitMask -type=.bed hg38.p12.2bit /dev/null hg38.p12.unmasked.2bit
     # chrom.sizes
     sort -k2nr,2nr chrom.sizes /hive/data/genomes/grcH38P12/chrom.sizes > chrom.sizes.p12
     # chromInfo
@@ -161,30 +161,42 @@
     rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
     ln -s /hive/data/genomes/hg38/goldenPath/bigZips/latest \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
 
     # 7/24/19: make correct links for chrom.sizes
     ln -sf /hive/data/genomes/hg38/chrom.sizes.initial \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/hg38.chrom.sizes
     ln -sf /hive/data/genomes/hg38/chrom.sizes.initial \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/initial/hg38.chrom.sizes
     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
+
+
 #########################################################################
 # 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
 #c9c5d621a52f96886fa9cd785c99248f