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.addChrMT.txt src/hg/makeDb/doc/hg19.addChrMT.txt
index c49696b..2b5d620 100644
--- src/hg/makeDb/doc/hg19.addChrMT.txt
+++ src/hg/makeDb/doc/hg19.addChrMT.txt
@@ -523,16 +523,30 @@
       # show table status like "windowmaskerSdust%";
       # drop table windowmaskerSdustBak;
       # quit
 
     # Double check:
     positionalTblCheck hg19 augustusGene
     positionalTblCheck hg19 cpgIslandExt
     positionalTblCheck hg19 gap
     positionalTblCheck hg19 genscan
     positionalTblCheck hg19 gold
     positionalTblCheck hg19 rmsk
     positionalTblCheck hg19 simpleRepeat
     positionalTblCheck hg19 windowmaskerSdust
 
 
+#############################################################################
+# Build perSeqMax file for gfServer (hgBlat) (DONE 2020-02-24 - 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.plusMT \
+    | grep -E '(MT|_(alt|fix|hap.*))$' \
+    | sed -re 's/^/hg19.2bit:/;' \
+      > hg19.altsAndFixes.p13.plusMT
+    # Link for blat server installation convenience:
+    ln -sf hg19.altsAndFixes.p13.plusMT altsAndFixes
+
+
 ##############################################################################