d93c426ef1ad5fbb32b754408599eaf380a199e5
max
  Tue Apr 21 13:34:58 2026 -0700
choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059

- Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML,
makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is
now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are
CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in
Methods.
- Wrap the existing CH1073 track in a choriCloneEnds superTrack and
add two new subtracks built from the parallel unique_concordant GFFs
at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ :
CH73  (99,141 placements, 23 oversize)
CH211 (70,231 placements, 46 oversize)
CH1073 is rebuilt with the same pipeline (210,777 placements).
- Build all three bigBeds with -extraIndex=name and register
searchTable / searchType bigBed stanzas with searchIndex name on each
subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...)
resolve from the Genome Browser position box.
- Single shared HTML description page; Methods now links to the NCBI
FTP source and to the UCSC makeDoc and scripts dir on GitHub.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
index dec93e8e127..64aaaff9427 100644
--- src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
+++ src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
@@ -17,20 +17,20 @@
 searchTable gold
 shortCircuit 1
 termRegex [ABCFLN][A-Z]+[0-9_][0-9]+(\.[0-9]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 track bacEndPairsLift
 shortLabel BAC End Pairs
 longLabel BAC End Pairs
 group map
 priority 15
 visibility hide
 type bigBed 12
 bigDataUrl /gbdb/danRer11/bacEndPairs/bacEndPairs.bb
 
-include ncbiCloneEndsCH1073.ra alpha
+include choriCloneEnds.ra alpha
 
 # change these two to switch to the new refSeqComposite 2018-02
 #include trackDb.refGene.ra public
 include ../../refSeqComposite.ra