44a3fed1a487ef0bbfb4d7443903661d81822350
max
  Mon May 30 06:36:56 2022 -0700
adding makedoc for REVEL tracks, refs #29475

diff --git src/hg/makeDb/doc/hg38/revel.txt src/hg/makeDb/doc/hg38/revel.txt
index 497b327..0b8d8b1 100644
--- src/hg/makeDb/doc/hg38/revel.txt
+++ src/hg/makeDb/doc/hg38/revel.txt
@@ -1,9 +1,14 @@
-#sed -i 's/chrom=/chrom=chr/' *.wig
-wget 'https://www.google.com/url?q=https%3A%2F%2Frothsj06.u.hpc.mssm.edu%2Frevel-v1.3_all_chromosomes.zip&sa=D&sntz=1&usg=AFQjCNHuQrCvuq--CoiCGwtDvQhBnTYj2Q'
+cd /hive/data/genomes/hg38/bed/revel
+wget https://rothsj06.u.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip
 unzip revel-v1.3_all_chromosomes.zip
+# there are two different revel scripts using entirely different strategies
+# they should have been merged, but once the hg19 one was working and tested, I didn't
+# want to mess with the hg19 script, and instead hacked it into an hg38 version.
 time python ~/kent/src/hg/makeDb/revel/revelToWig-hg38.py ../../chrom.sizes revel_with_transcript_ids 
 wigToBigWig a.wig ../../chrom.sizes a.bw &
 wigToBigWig t.wig ../../chrom.sizes t.bw &
 wigToBigWig c.wig ../../chrom.sizes c.bw  &
 wigToBigWig g.wig ../../chrom.sizes g.bw &
+bedSort overlap.bed overlap.bed
+bedToBigBed overlap.bed -as=~/kent/src/hg/makeDb/revel/revel.as ../../../chrom.sizes overlap.bb -tab -type=bed8+
 rm *.wig -f