a80b1e18948fdd1bccec83660a5ca3db9628f95a
jcasper
  Thu Mar 18 23:10:50 2021 -0700
Supporting files and makedoc update for DECIPHER haploinsufficiency, refs #25707

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index ed4e1f1..86a0199 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34223,38 +34223,41 @@
 cd /hive/data/outside/decipher/haploinsufficiency
 wget https://decipher.sanger.ac.uk/files/downloads/HI_Predictions_Version3.bed.gz
 filePath=`pwd`/HI_Predictions_Version3.bed.gz
 
 # zcat | head shows the file is nearly ready to go, but could benefit from a bit of reorganization
 # (also floating point score values don't work for some bed processors)
 
 mkdir -p /hive/data/genomes/hg19/bed/decipherHaplo
 cd /hive/data/genomes/hg19/bed/decipherHaplo
 
 printf 'chomp;
 @fields = split /\t/;
 ($gene, $score, $pct) = split /\|/, $fields[3];
 $fields[3] = $gene;
 $fields[4] = 0;
+$rgb = $fields[8];
+$rgb =~ s/^(\d+),(\d+),0$/$1,$2,$1/;  # change red/green to magenta/green
+$fields[8] = $rgb;
 push @fields, ($pct, $score);
 push @fields, ("$gene, HI: $pct");
 print join ("\t", @fields) . "\n";
 ' > parse.pl
 
 zcat $filePath | tail -n +2 | perl -nf parse.pl | bedSort stdin HI_Predictions.bed
 
-bedToBigBed HI_Predictions.bed -type=bed9+3 -as=$HOME/kent/src/hg/lib/haploinsufficiency.as -tab ../../chrom.sizes haploinsufficiency.bb
+bedToBigBed HI_Predictions.bed -type=bed9+2 -as=$HOME/kent/src/hg/lib/haploinsufficiency.as -tab ../../chrom.sizes haploinsufficiency.bb
 
 mkdir -p /gbdb/hg19/bbi/haploins/
 cd /gbdb/hg19/bbi/haploins/
 ln -s /hive/data/genomes/hg19/bed/decipherHaplo/haploinsufficiency.bb .
 
 
 #############################################################################
 # skinSoleBoldo JimK 01-14-2020
 # This describes how we got the skinSoleBoldo data set into the
 # Genome Browser from the Cell Browser.
 #############################################################################
 
 # Create working directory and go there
 mkdir /hive/data/genomes/hg19/bed/singleCell/skinSoleBoldo
 cd /hive/data/genomes/hg19/bed/singleCell/skinSoleBoldo