e0dcc4f87e4051aa6094860e0f2a9536e90c97c9
markd
  Thu Jan 27 18:02:39 2022 -0800
import of GENCODE V40lift37 pre-release

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index a38ce53..1890490 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -970,15 +970,42 @@
     These are missing from
 	 data/release_39lift37/gencode.v39lift37.metadata.Transcript_source.gz
          data/release_39lift37/gencode.v39lift37.metadata.Gene_source.gz
 
      this is the weird cases of SPRV3 which has now has a transcript past the PAR
 
       echo -e 'ENST00000302805.2\tensembl_havana_transcript_homo_sapiens' >> tables/wgEncodeGencodeTranscriptSourceV39lift37.tab 
       echo -e 'ENSG00000168939.6\tensembl_havana_transcript_homo_sapiens' >> tables/wgEncodeGencodeGeneSourceV39lift37.tab 
       rm loaded/wgEncodeGencode*Support*
       (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.4.out&
 
     # commit all
     jkmake alpha DBS=hg19
 
 ##############################################################################
+2022-01-16: import of UCSC GENCODE group processing of GENCODE V40lift37 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/gencodeV40lift37/hgcImportPre
+    pushd /hive/data/genomes/hg19/bed/gencodeV40lift37/hgcImportPre
+
+    (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/bin/gencodeGenerateTrackDbs hg19 40lift37 106 Feb 2022'
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV40lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV40lift37/hgcImportPre
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+    jkmake alpha DBS=hg19
+
+##############################################################################