9e65e54f0f956ea44785df0427f0f457fcfbb34c
max
  Fri Dec 13 05:34:09 2024 -0800
fix for hg19 revel track, refs #34947

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 10a8186..bccaceb 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34607,34 +34607,35 @@
 | scaRna  |   21 |
 +---------+------+
 
     # backup old table and compare to new one before rename. Should be only miRNA update:
     hgsql -Ne "select * from wgRna" hg19 | cut -f2- > wgRna.backup
     comm -23 <(sort -k1 -k2n wgRna2021-02-18.bed) <(sort -k1 -k2n wgRna.backup) | cut -f9 | sort -u
 miRNA
 
     # rename wgRnaNew table:
     hgsqlSwapTables -dropTable3 hg19 wgRnaNew wgRna wgRnaOld
 
 ##############################################################################
 # Add Revel track, Max, Thu Apr 15 03:33:49 PDT 2021
 # UPDATE: Adding overlap track after request from NHS, Max, Mon May 23 07:50:02 PDT 2022
 # There was a new REVEL release with transcript IDs! Obviously no one told us
+# Update Dec 2024: Using the hg38 code now, so all overlaps are nicely condensed into one feature
 cd /hive/data/genomes/hg19/bed/revel
 wget https://rothsj06.u.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip
 unzip *.zip
-python ~/kent/src/hg/makeDb/revel/revelToWig.py revel_with_transcript_ids hg19 
+python3 ~/kent/src/hg/makeDb/revel/revelToWig-hg38.py revel_with_transcript_ids hg19 
 wigToBigWig t.wig ../../chrom.sizes t.bw &
 wigToBigWig c.wig ../../chrom.sizes c.bw  &
 wigToBigWig a.wig ../../chrom.sizes a.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+
 
 ##############################################################################
 # LASTZ human/hg19 Gorilla/gorGor6 - (DONE - 2021-06-28 - Gerardo)
     mkdir /hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28/
     cd /hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28/
 
     printf '# human vs gorilla
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 BLASTZ_T=2