src/hg/makeDb/doc/aplCal1.txt 1.11

Index: src/hg/makeDb/doc/aplCal1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/aplCal1.txt,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/hg/makeDb/doc/aplCal1.txt	20 Jan 2010 04:32:17 -0000	1.10
+++ src/hg/makeDb/doc/aplCal1.txt	4 Feb 2010 19:35:11 -0000	1.11
@@ -522,9 +522,29 @@
           hgsql aplCal1 -e 'select distinct(file) from quality'
 
     # added to all.joiner both $gbd and $chainDest
 
+############################################################################
+# Creating the chain/net trackDb.ra entry (DONE - 2010-02-04 - Galt)
 
-#######################################################################
-#  see hg19.txt for chain to hg19 assembly
+#add simplified lastz symlink to hg19
+    cd /hive/data/genomes/hg19/bed
+    ln -s lastzAplCal1.2009-06-08/ lastz.aplCal1
+    findScores.pl hg19 aplCal1
+#looking in file:
+#  /hive/data/genomes/hg19/bed/lastz.aplCal1/axtChain/run/chain.csh
+#-scoreScheme=/scratch/data/blastz/HoxD55.q
+#matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+#-minScore=5000
+#-linearGap=loose
 
+    cd kent/src/hg/makeDb/trackDb
+    vi trackDb.chainNet.ra 
+#cloned fr2 setting,  substituted aplCal1 for fr2 and AplCal1 for Fr2
+# checked that these settings match the above output
+#matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+#chainMinScore 5000 
+#chainLinearGap loose
+
+    make DBS=hg19
+    cvs commit -m 'adding aplCal1 chain/net' trackDb.chainNet.ra