src/hg/makeDb/doc/aplCal1.txt 1.2

Index: src/hg/makeDb/doc/aplCal1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/aplCal1.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/doc/aplCal1.txt	13 May 2009 20:56:14 -0000	1.1
+++ src/hg/makeDb/doc/aplCal1.txt	14 May 2009 00:26:13 -0000	1.2
@@ -49,4 +49,20 @@
 
 # Edit and check-in templates for description.html, gold.html, gap.html, aplCal1/trackDb.ra
 
 
+# repeat mask
+time doRepeatMasker.pl aplCal1 > & doRepeatMasker.pl.out &
+
+
+# simple repeat masker trf
+time doSimpleRepeat.pl aplCal1 > & doSimpleRepeat.pl.out &
+
+# make final masked .2bit
+[hgwdev:aplCal1> twoBitMask aplCal1.rmsk.2bit -add bed/simpleRepeat.2009-05-13/trfMask.bed aplCal1.2bit
+#Warning: BED file bed/simpleRepeat.2009-05-13/trfMask.bed has >=13 fields
+#which means it might contain block coordinates, but this program uses only the
+#first three fields (the entire span -- no support for blocks).
+
+ln -s /cluster/data/aplCal1/aplCal1.2bit /gbdb/aplCal1/
+
+