src/hg/makeDb/doc/hg19.txt 1.76

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.75
retrieving revision 1.76
diff -b -B -U 4 -r1.75 -r1.76
--- src/hg/makeDb/doc/hg19.txt	26 Jan 2010 19:41:22 -0000	1.75
+++ src/hg/makeDb/doc/hg19.txt	28 Jan 2010 23:49:54 -0000	1.76
@@ -8439,9 +8439,20 @@
 
 # remove variants that are homozygous matches to hg19
 
 ########################################################################
-# CRG MAPABILITY (2010-01-19, hartera, in progress)
+# CRG MAPABILITY (2010-01-19 - 2010-01-28, hartera, DONE)
+# Data was provided by Thomas Derrien (thomas.derrien.crg.es) and Paolo Ribeca
+# from the Guigo lab at the Center for Genomic Regulation (CRG) in Barcelona. 
+# Data was produced using their GEM mapper aligner taking sliding k-mers 
+# window of the human genome that were mapped back onto the genome with up 
+# to 2mismatches. For each window, a mappability score is computed 
+# S = 1/(nb of match_found) and the BigWig index was created according to 
+# this score. 
+# 2010-01-26 Loaded tables and added data to /gbdb/
+# 2010-01-28 Changed the table names to have the "enc" prefix for consistency
+# going forward with hg19 ENCODE tracks. Added trackDb entry for this 
+# ENCODE Mapability track. 
     
     mkdir -p /hive/data/genomes/hg19/bed/crgMapability
     cd /hive/data/genomes/hg19/bed/crgMapability
 cat << 'EOF' > temp
@@ -8478,4 +8489,19 @@
         hgsql hg19 -e "drop table if exists crgMapabilityAlign${mer}; \
      create table crgMapabilityAlign${mer} (fileName varchar(255) not null); \
      insert into crgMapabilityAlign${mer} values ('/gbdb/hg19/bbi/${nf}');"
      end
+
+     # 2010-01-28
+     # Renamed the tables to have a enc prefix for consistency going 
+     # forward with hg19.
+     cd /hive/data/genomes/hg19/bed/crgMapability
+     hgsql -Ne 'show tables like "crg%";' hg19 > tables.txt
+     foreach t (`cat tables.txt`)
+        set g=`echo $t | sed -e 's/c/C/'`
+        hgsql -e "alter table ${t} rename enc${g};" hg19
+     end 
+     # Added a trackDb entry for this ENCODE Mapability 
+     # track in kent/src/hg/makeDb/trackDb/human/hg19/trackDb.ra 
+     # Copied track from the hg18/trackDb.wgEncode.ra entry.  
+     # use bigWigInfo to check min and max values. 
+     # This entry will be moved to a trackDb.enc.ra file in the future.