src/hg/makeDb/doc/mm9.txt 1.94

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.93
retrieving revision 1.94
diff -b -B -U 4 -r1.93 -r1.94
--- src/hg/makeDb/doc/mm9.txt	8 May 2009 21:26:54 -0000	1.93
+++ src/hg/makeDb/doc/mm9.txt	22 May 2009 21:32:06 -0000	1.94
@@ -9342,4 +9342,25 @@
 # refGene:cds 1.205%, blastHg18KG 1.156%, both 0.940%, cover 78.04%, enrich 67.52x
 
     rm -rf blastOut
 #end tblastn
+
+#############################################################################
+# LASTZ Swap Human Hg19 (DONE - 2009-05-14 - Hiram)
+    #	the original
+    cd /hive/data/genomes/hg19/bed/lastzMm9.2009-05-13
+    cat fb.hg19.chainMm9Link.txt 
+    #	1022734273 bases of 2897316137 (35.299%) in intersection
+
+    #	and the swap
+    mkdir /hive/data/genomes/mm9/bed/blastz.hg19.swap
+    cd /hive/data/genomes/mm9/bed/blastz.hg19.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/hg19/bed/lastzMm9.2009-05-13/DEF \
+	-swap -noLoadChainSplit -syntenicNet \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+    #	real    131m58.763s
+    cat fb.mm9.chainHg19Link.txt 
+    #	1013880568 bases of 2620346127 (38.693%) in intersection
+
+#############################################################################