4440223fad68a002964802e0ecf3b1b94cb28503
markd
  Sat Nov 16 10:11:29 2019 -0800
import of gencode V33 prerelase

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 44448a1..5eeea9b 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -551,15 +551,59 @@
     Changes:
     wgEncodeGencode2wayConsPseudoV32.gp 
     wgEncodeGencodeAttrsV32.tab
     wgEncodeGencodePolyaV32.gp
     wgEncodeGencodeTagV32.tab
     only attrs and maybe tags matter to hgGene gencode
 
     mkdir pre-diffs
     diff ../gencodeV32pre/tables/wgEncodeGencodeAttrsV32.tab tables/wgEncodeGencodeAttrsV32.tab >pre-diffs/wgEncodeGencodeAttrsV32.diff
     diff ../gencodeV32pre/tables/wgEncodeGencodeTagV32.tab tables/wgEncodeGencodeTagV32.tab >pre-diffs/wgEncodeGencodeTagV32.diff
 
     # wgEncodeGencodeAttrsV32: experimental conformation level changed on a few pseudogenes
     # wgEncodeGencodeTagV32: pseudo_consens changed on a few pseudogenes.
 
 #########################################################################
+2019-11-15: import of UCSC GENCODE group processing of GENCODE V32 (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/hg38/bed/gencodeV33
+    pushd /hive/data/genomes/hg38/bed/gencodeV33
+
+    (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 hg38 33 40 'Nov 2019'
+
+    # If being pushed public, update 'Release Notes' in
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    make DBS=hg38
+
+    ## only if being pushed to RR:
+    # edit all.joiner to add ~/tmp/gencodeV33.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV33
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+
+#########################################################################
+
+if fgrep Error: check/joiner.out ; then false;  else true; fi
+Error: 6 of 20572 elements (0.029%) of hg38.wgEncodeGencodePseudoGeneV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2645 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+Error: 857 of 226969 elements (0.378%) of hg38.wgEncodeGencodeCompV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2640 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+Error: 703 of 100360 elements (0.700%) of hg38.wgEncodeGencodeBasicV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2635 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+Error: 703 of 100360 elements (0.700%) of hg38.wgEncodeGencodeBasicV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2635 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+Error: 857 of 226969 elements (0.378%) of hg38.wgEncodeGencodeCompV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2640 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+Error: 6 of 20572 elements (0.029%) of hg38.wgEncodeGencodePseudoGeneV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2645 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+make: *** [joinerCheck] Error 1
+
+Error: 857 of 226969 elements (0.378%) of hg38.wgEncodeGencodeCompV33.name are not in key wgEncodeGencodeAttrsV33.transcriptId line 2640 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
+hgsql  hg38 -Ne 'select name from wgEncodeGencodeCompV33 where name not in  (select transcriptId  from wgEncodeGencodeAttrsV33)' >~/tmp/comp.ids