da323191c57c36932ad1751af87b59b71b836501
markd
  Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073

diff --git src/hg/makeDb/doc/hg38/hgnc.txt src/hg/makeDb/doc/hg38/hgnc.txt
index 04638516fb9..19f55c703fc 100644
--- src/hg/makeDb/doc/hg38/hgnc.txt
+++ src/hg/makeDb/doc/hg38/hgnc.txt
@@ -142,18 +142,47 @@
 # modified mgd_id to be lstring instead of string since it was 493 chars that overflowed string which takes 255 char max.
 # changed strand description to "+ or - for strand"
 
 # let's do this thing!
 bedToBigBed -extraIndex=name -tab -type=bed9+53 input.bed /cluster/data/hg38/chrom.sizes hgnc.hg38.bb -as=$HOME/kent/src/hg/lib/hgncBig62.as
 
 # put the files into /gbdb
 mkdir -p /gbdb/hg38/hgnc
 rm -rf /gbdb/hg38/hgnc/hgnc.bb
 ln -s `pwd`/hgnc.hg38.bb /gbdb/hg38/hgnc/hgnc.bb 
 
 rm -rf /gbdb/hg38/hgnc/search.ix /gbdb/hg38/hgnc/search.ixx
 ln -s `pwd`/search.hg38.ix /gbdb/hg38/hgnc/search.ix
 ln -s `pwd`/search.hg38.ixx /gbdb/hg38/hgnc/search.ixx
 
-##################################
+#################################################################################
+2025-07-23:  markd #36073
+
+Replace previous build method with one to based on GENCODE, RefSeq curated,
+and RefSeq other.  This address various problems dealing with the complexity
+of NCBI gene2accession to find the locations. See #36073.
+
+cd /cluster/data/hg38/bed/hgnc/
+mkdir build.2025-07-24
+cd build.2025-07-24
+
+wget -nv https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
+
+~/kent/src/hg/makeDb/outside/hgnc/hgncToBigBed --unmappedTsv=hgnc.unmapped.tsv hg38 V48 hgnc_complete_set.txt hgnc.bed hgnc.bb search locus_type.filter.txt
+
+# Note it is expected that there will be unmapped:
+#  - a few protein-coding genes not in the assembly
+#  - pseudogenes and non-coding genes not in GENCODE or RefSeq for unknown reasons
+#  - locus_group `other' types that are not mapped.
+
+# put the files into /gbdb
+mkdir -p /gbdb/hg38/hgnc
+ln -sf $(realpath hgnc.bb search.ix search.ixx) /gbdb/hg38/hgnc/
+
+# double check
+ls -l /gbdb/hg38/hgnc/
+file  /gbdb/hg38/hgnc/*
 
+# edit trackDb/human/trackDb.ra to set  filterValues.locus_type
+# from the locus_type.filter.txt file
 
+#################################################################################