f86cc1e3f913432f81ad47733aae8e78ab9500c6
markd
  Mon May 27 12:06:58 2019 -0700
output total number of aligned bases in pslStats -overallStats

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index c38efd2..813647b 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33460,16 +33460,46 @@
     # itemCount: 38,185
     # primaryDataSize: 30,841,362
     # primaryIndexSize: 6,892
     # zoomLevels: 8
     # chromCount: 24
     # basesCovered: 580,564,080
     # meanDepth (of bases covered): 3.668451
     # minDepth: 1.000000
     # maxDepth: 81.000000
     # std of depth: 5.825349
 
     # link into gbdb
     mkdir -p /gbdb/hg19/dgv
     ln -s `pwd`/dgvGold.bb /gbdb/hg19/dgv/
 
+#############################################################################
+2019-05-23: import of UCSC GENCODE group processing of GENCODE V31lift37 (markd)
+    # import of pre-release, it will be promoted if there are no changes in the final 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/gencodeV31lift37-pre
+    pushd /hive/data/genomes/hg19/bed/gencodeV31lift37-pre
+    (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 31lift37 97 'June 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/gencodeV31lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV31lift37
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+
 ##############################################################################