06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/makeDb/doc/calJac3.txt src/hg/makeDb/doc/calJac3.txt
index e676988..a891718 100644
--- src/hg/makeDb/doc/calJac3.txt
+++ src/hg/makeDb/doc/calJac3.txt
@@ -3290,16 +3290,37 @@
     cd /hive/data/genomes/rheMac8/bed/blastz.calJac3.swap
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/calJac3/bed/lastzRheMac8.2017-08-08/DEF \
 	-swap -syntenicNet -chainMinScore=3000 -chainLinearGap=medium \
 	-workhorse=hgwdev -smallClusterHub=ku \
 	-bigClusterHub=ku) > swap.log 2>&1
     #	real    265m36.306s
 
     cat fb.rheMac8.chainCalJac3Link.txt
     #	2208994431 bases of 3142093174 (70.303%) in intersection
 
     time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` rheMac8 calJac3) \
 	> rbest.log 2>&1 &
     # real    1183m6.027s
 
-############################################################################
+##############################################################################
+# LIFTOVER TO calJac4 (DONE - 2020-09-04 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/calJac3/bed/blat.calJac4.2020-09-04
+    cd /hive/data/genomes/calJac3/bed/blat.calJac4.2020-09-04
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/calJac3/calJac3.2bit \
+        -targetSizes=/hive/data/genomes/calJac3/chrom.sizes \
+        -ooc=/hive/data/genomes/calJac3/jkStuff/calJac3.11.ooc \
+         calJac3 calJac4
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/calJac3/calJac3.2bit \
+        -targetSizes=/hive/data/genomes/calJac3/chrom.sizes \
+        -ooc=/hive/data/genomes/calJac3/jkStuff/calJac3.11.ooc \
+         calJac3 calJac4) > doLiftOverToCalJac4.log 2>&1
+    # real    257m56.056s
+
+    # see if the liftOver menus function in the browser from calJac3 to calJac4
+
+##############################################################################