src/hg/makeDb/doc/hg19.txt 1.75

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.74
retrieving revision 1.75
diff -b -B -U 4 -r1.74 -r1.75
--- src/hg/makeDb/doc/hg19.txt	25 Jan 2010 19:16:13 -0000	1.74
+++ src/hg/makeDb/doc/hg19.txt	26 Jan 2010 19:41:22 -0000	1.75
@@ -8438,6 +8438,44 @@
 # liftOver track files in /hive/data/genomes/hg18/bed/pgSnp/
 
 # remove variants that are homozygous matches to hg19
 
-
 ######################################################################## 
+# CRG MAPABILITY (2010-01-19, hartera, in progress)
+    
+    mkdir -p /hive/data/genomes/hg19/bed/crgMapability
+    cd /hive/data/genomes/hg19/bed/crgMapability
+cat << 'EOF' > temp
+#!/bin/tcsh -ef
+http://genome.imim.es/~tderrien/UCSC_Tracks/ALL_mappablity_hg19_H.sapiens.genome.hg19.main.mappability-36.bw.bz2
+http://genome.imim.es/~tderrien/UCSC_Tracks/ALL_mappablity_hg19_H.sapiens.genome.hg19.main.mappability-50.bw.bz2
+http://genome.imim.es/~tderrien/UCSC_Tracks/ALL_mappablity_hg19_H.sapiens.genome.hg19.main.mappability-75.bw.bz2
+http://genome.imim.es/~tderrien/UCSC_Tracks/ALL_mappablity_hg19_H.sapiens.genome.hg19.main.mappability-100.bw.bz2
+'EOF'
+
+    awk '{if ($0 ~ /#/) print; else print "wget --timestamping \"" $0 "\"";}' \
+        temp > download.csh
+    rm temp
+    chmod +x download.csh
+    ./download.csh >& download.log &
+
+     # Add the data to /gbdb/ and load the file names into tables (2010-01-26)
+     cd /hive/data/genomes/hg19/bed/crgMapability
+     bunzip2 *.bz2
+
+     # Add data to gbdb
+     mkdir -p /gbdb/hg19/bbi/
+     # Symlink files with names as crgMapabilityAlignXmer.bw to /gbdb/hg18/bbi
+     # and load file name into a table - one per dataset. Each table 
+     # represents a subtrack.
+     foreach f (`ls *.bw`)
+        echo $f
+        set g=`echo $f | cut -d "-" -f2`
+        set num=`echo $g | cut -d "." -f1`
+        set mer=`echo "${num}mer"`
+        set nf=`echo "crgMapabilityAlign${mer}.bw"`
+        echo $nf
+        ln -s `pwd`/${f} /gbdb/hg19/bbi/${nf}
+        hgsql hg19 -e "drop table if exists crgMapabilityAlign${mer}; \
+     create table crgMapabilityAlign${mer} (fileName varchar(255) not null); \
+     insert into crgMapabilityAlign${mer} values ('/gbdb/hg19/bbi/${nf}');"
+     end