af06f485943b58470dccd7c832b97042f0c8ddb8
gperez2
  Sun Jan 18 21:44:31 2026 -0800
Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779

diff --git src/hg/makeDb/doc/hg38/ncbiRefSeq.txt src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
index 601a838fce7..b911944d703 100644
--- src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
+++ src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
@@ -221,30 +221,31 @@
 # updated Dec 2020
 # updated Aug 2023
 # updated May 2024
 # updated Dec 2024
 year=2024
 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p14.2023-11-23/
 # change in 2019: ignore the version numbers, otherwise only 1815 transcripts left, big update by HGMD in 2019?
 # adding "." so NM_123 doesn't match NM_123123                                                                             
 cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | cut -d. -f1 | sort -u | awk '{print $1"."}' > hgmdTranscripts.txt
 zcat process/hg38.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
 hgLoadGenePred -genePredExt hg38 ncbiRefSeqHgmd hgmd.curated.gp
 # wc -l says:
 10772 hgmd.curated.gp for the 2021 version
 12602 hgmd.curated.gp for the 2023 version
 15167 hgmd.curated.gp for the 2024 version
+15691 hgmd.curated.gp for the 2025 version (See hg38/hgmd.txt for details)
 #############################################################################
 # ncbiRefSeq.p13 update (DONE - 2019-12-06 - Hiram)
 
 # current version information
     cat /gbdb/hg38/ncbiRefSeq/ncbiRefSeqVersion.txt
     # NCBI Homo sapiens Annotation Release 109 (2018-03-29)
 
 # Version information from the file:
 
 # /hive/data/outside/ncbi/genomes/refseq/vertebrate_mammalian/Homo_sapiens/
 #   all_assembly_versions/GCF_000001405.39_GRCh38.p13/
 #   GCF_000001405.39_GRCh38.p13_genomic.gff.gz
 
 #!annotation-date 09/05/2019
 #!annotation-source NCBI Homo sapiens Updated Annotation Release 109.20190905