src/hg/makeDb/doc/hg18.txt 1.396

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.395
retrieving revision 1.396
diff -b -B -U 4 -r1.395 -r1.396
--- src/hg/makeDb/doc/hg18.txt	26 Jan 2010 19:39:35 -0000	1.395
+++ src/hg/makeDb/doc/hg18.txt	28 Jan 2010 23:48:44 -0000	1.396
@@ -29279,15 +29279,19 @@
     hgLoadBed hg18 gwasCatalog gwasCatalog.bed \
       -tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
 
 #############################################################################
-# CRG MAPABILITY (2010-01-19, hartera, in progress)
-# Data was provided by Thomas Derrien (thomas.derrien.crg.es) 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 2mimatches.
-# For each window, a mappability score is computed S = 1/(nb of match_found)
-# and the BigWig index was created according to this score.
+# 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 wgEncode prefix for consistency. 
+# Added trackDb entry for the subtracks to the ENCODE Mapability track entry.
     
      mkdir -p /hive/data/genomes/hg18/bed/crgMapability
      cd /hive/data/genomes/hg18/bed/crgMapability
 cat << 'EOF' > temp
@@ -29325,4 +29329,17 @@
         hgsql hg18 -e "drop table if exists crgMapabilityAlign${mer}; \
      create table crgMapabilityAlign${mer} (fileName varchar(255) not null); \
      insert into crgMapabilityAlign${mer} values ('/gbdb/hg18/bbi/${nf}');"
      end
+
+     # 2010-01-28. 
+     # Renamed the tables to have a wgEncode prefix for consistency. 
+     cd /hive/data/genomes/hg18/bed/crgMapability
+     hgsql -Ne 'show tables like "crg%";' hg18 > 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 subtrack of the ENCODE Mapability 
+     # track in kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
+     # use bigWigInfo to check min and max values. 
+