db3443c1060188f5e7abe8e640e3f245bd7f8cb7
markd
  Thu Dec 19 11:57:34 2019 -0800
load of gencode V33lift37 prerelease

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index c3ea49c..4181506 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33800,16 +33800,44 @@
 #      int[blockCount] blockStarts; "0-based start position of each exon"
 #      string _mouseOver;  "Mouseover label"
 #      string geneName;   "Associated Gene symbol"
 #      string synonymous; "Synonymous metrics"
 #      string missense;   "Missense metrics"
 #      string pLoF;       "Predicted Loss of Function metrics
 #      )
 
 sizes=/hive/data/genomes/hg19/chrom.sizes
 bedToBigBed -type=bed12+5 -as=pliMetrics.as -tab -extraIndex=name,geneName pliByGene.bed $sizes pliByGene.bb
 bedToBigBed -type=bed12+5 -as=pliMetrics.as -tab -extraIndex=name,geneName pliByTranscript.bed $sizes pliByTranscript.bb
 cd /gbdb/hg19/gnomAD/pLI/
 ln -s /hive/data/outside/gnomAD.2/constraint/pliByGene.bb
 ln -s /hive/data/outside/gnomAD.2/constraint/pliByTranscript.bb
 #########################################################################
+2019-11-17: import of UCSC GENCODE group processing of GENCODE V33lift37 (markd)
+    # PRE-RELEASE
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg19/bed/gencodeV33lift37
+    pushd /hive/data/genomes/hg19/bed/gencodeV33lift37
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg19 33lift37 99 'Nov 2019'
 
+    # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
+    # to describe new release. [ONLY if it's going to be pushed]
+
+    # edit human/hg19/trackDb.wgEncode.ra to add new .ra file include
+    make DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV33lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV33lift37
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+##############################################################################