12a7062ec0510b37e2cb6e8c294b53d2b0af69e0
markd
  Tue Jan 21 18:24:46 2020 -0800
import of gencodeV33lift37

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index d86cbd6..d42d412 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33801,32 +33801,32 @@
 #      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
+2019-11-17: import of UCSC GENCODE group processing of GENCODE V33lift37 PRE-RELEASE (markd)
+    # 
     # 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'
@@ -33959,15 +33959,45 @@
     # pass2 - checking and writing primary data (6507 records, 17 fields): 134 millis
     # only a few genes:
     cut -f13 missenseConstrained.bed | sort | uniq | wc -l
     # 2700
     ln -s /gbdb/hg19/gnomAD/missenseConstrained.bb missenseConstrained.bb
 
 ##############################################################################
 # adding RefSeq Select to NCBIRefSeq, Max, Feb 17 2020
 cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2019-11-21
 zcat download/*_genomic.gff.gz | egrep 'tag=(RefSeq|MANE) Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
 cat process/hg19.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqSelect refseqSelect.curated.gp
 wc -l refseqSelect.curated.gp
 21436 refseqSelect.curated.gp
 ##############################################################################
+2020-01-16: import of UCSC GENCODE group processing of GENCODE V33lift37 (markd)
+    # deprecate pre-release
+    mv /hive/data/genomes/hg19/bed/gencodeV33lift37 /hive/data/genomes/hg19/bed/gencodeV33lift37Pre
+    # 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 'Jan 2020'
+
+    # 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.gencode.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
+##############################################################################