f7d9c08f80220550ac2f58cbb9e17e957c5f3e51
angie
  Wed Feb 19 09:35:46 2020 -0800
hg19 uses gc5Base not gc5BaseBw -- add p13 + chrMT data to gc5Base.  refs #24648

diff --git src/hg/makeDb/doc/hg19.addChrMT.txt src/hg/makeDb/doc/hg19.addChrMT.txt
index 44a8a20..1307af0 100644
--- src/hg/makeDb/doc/hg19.addChrMT.txt
+++ src/hg/makeDb/doc/hg19.addChrMT.txt
@@ -1,18 +1,19 @@
 # for emacs: -*- mode: sh; -*-
 
 # This file describes how hg19 was extended with the rCRS mitochondrial sequence (NC_012920) as chrMT
+# Redmine #24648
 
 ##############################################################################
 # Get NC_012920.1 sequence, rename to chrMT. (DONE - 2020-01-14 - Angie)
     mkdir /hive/data/genomes/hg19/MT
     cd /hive/data/genomes/hg19/MT
     wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/current/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_structure/non-nuclear/assembled_chromosomes/FASTA/chrMT.fna.gz
     wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/current/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_structure/non-nuclear/assembled_chromosomes/AGP/chrMT.comp.agp.gz
     zcat chrMT.fna.gz \
     | sed -e 's/^>NC_012920.1.*/>chrMT/' \
       > chrMT.fa
     zcat chrMT.comp.agp.gz \
     | grep -v ^# \
     | sed -e 's/^NC_012920.1/chrMT/' \
       > chrMT.agp
 
@@ -432,15 +433,30 @@
     cd /hive/data/genomes/hg19/bed/gtex
     cp gtexGeneV6.plusP13.bed gtexGeneV6.plusP13.plusMT.bed
     grep ^chrM gtexGeneV6.bed | sed -re 's/chrM\t/chrMT\t/;' >> gtexGeneV6.plusP13.plusMT.bed
 
     hgLoadBed -noBin -type=bed6+ -sqlTable=$HOME/kent/src/hg/lib/gtexGeneBed.sql -renameSqlTable \
         hg19 gtexGene gtexGeneV6.plusP13.plusMT.bed
 
     grep -w chrM gtexGeneModelV6.initial.gp \
     | sed -re 's/chrM\t/chrMT\t/' \
       > gtexGeneModelV6.MT.gp
     sort -k2,2 -k3n,3n gtexGeneModelV6.initial.gp gtexGeneModelV6.p13.gp gtexGeneModelV6.MT.gp \
     | hgLoadGenePred hg19 gtexGeneModel stdin
 
 
 ##############################################################################
+# Oops update original wiggle gc5Base (gc5BaseBw is not released for hg19) (DONE 2020-02-18 - Angie)
+    # Redmine #24648 notes 18 & 19
+    cd /hive/data/genomes/hg19/bed/gc5Base/
+    wigEncode hg19.p13.plusMT.gc5Base.wigVarStep.gz gc5Base.p13.plusMT.{wig,wib}
+    # Install
+    ln -s `pwd`/gc5Base.p13.plusMT.wib /gbdb/hg19/wib
+    hgLoadWiggle -pathPrefix=/gbdb/hg19/wib hg19 gc5Base gc5Base.p13.plusMT.wig
+    # Also update the gc5Base varStep wiggle download file:
+    cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/gc5Base
+    ln -sf /hive/data/genomes/hg19/bed/gc5Base/hg19.p13.plusMT.gc5Base.wigVarStep.gz \
+      hg19.gc5Base.txt.gz
+    md5sum hg19.gc5Base.txt.gz > md5sum.txt
+
+
+##############################################################################