db0877a0f789518c170e95923feee7ad95e15b55
markd
  Sun Mar 22 09:14:47 2020 -0700
import of GENCODE V34 and VM25 prereleases

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index f438497..412f340 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34246,15 +34246,43 @@
      109025 INS x 
         748 INV x 
        1108 MCNV x
           1 SVTYPE
 
     # add colors based on gnomad website and get in to proper bed9+
     for f in *.bed4Plus; do out=${f/.bed4Plus/}; bedClip -truncate $f $chromSizes stdout | ./gnomadSvToUcsc.awk | sort -k1,1 -k2,2n > $out.bed9Plus; done
 
     chromSizes=/hive/data/genomes/hg19/chrom.sizes
     for f in *.bed9Plus; do out=${f/.bed9Plus/}; bedToBigBed -tab -type=bed9+1 -as=gnomadSv.as $f $chromSizes $out.bb; done
     mkdir -p /gbdb/hg19/gnomAD/structuralVariants/ 
     cd /gbdb/hg19/gnomAD/structuralVariants/
     cp -s /hive/data/outside/gnomAD.2/structuralVariants/*.bb .
 
 ##############################################################################
+2020-03-11: import of UCSC GENCODE group processing of GENCODE V34lift37 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/gencodeV34lift37Pre
+    pushd /hive/data/genomes/hg19/bed/gencodeV34lift37Pre
+    (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 34lift37 100 'March 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/gencodeV34lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV34lift37Pre
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+##############################################################################