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/choriCloneEnds.ra src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra
new file mode 100644
index 00000000000..3d6b61152b9
--- /dev/null
+++ src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra
@@ -0,0 +1,87 @@
+track choriCloneEnds
+superTrack on
+shortLabel CHORI Clones
+longLabel CHORI zebrafish BAC library clone end placements (NCBI Clone DB unique_concordant)
+group map
+html choriCloneEnds
+
+    track choriCloneEndsCH1073
+    parent choriCloneEnds
+    shortLabel CHORI CH1073
+    longLabel CHORI CH1073 (RZPD-1073/DanioKey) BAC library clone end placements, unique concordant
+    type bigBed 6 +
+    bigDataUrl /gbdb/danRer11/choriCloneEnds/CH1073.bb
+    color 60,100,160
+    visibility pack
+    url https://zfin.org/search?q=$$
+    urlLabel ZFIN clone search:
+    searchIndex name
+    filterValues.concordant TRUE,FALSE
+    filterLabel.concordant End-pair concordance
+    filterType.concordant multipleListOnlyOr
+    filterValues.unique TRUE,FALSE
+    filterLabel.unique Unique placement
+    filterType.unique multipleListOnlyOr
+    filterValues.oversize TRUE,FALSE
+    filterLabel.oversize Oversize placement (>500kb)
+    filterType.oversize multipleListOnlyOr
+    skipFields score,strand,placementMethod
+    html choriCloneEnds
+
+searchTable choriCloneEndsCH1073
+searchType bigBed
+searchPriority 20
+
+    track choriCloneEndsCH73
+    parent choriCloneEnds
+    shortLabel CHORI CH73
+    longLabel CHORI CH73 (RZPD-73 / DanioKey Pilot) BAC library clone end placements, unique concordant
+    type bigBed 6 +
+    bigDataUrl /gbdb/danRer11/choriCloneEnds/CH73.bb
+    color 160,60,60
+    visibility pack
+    url https://zfin.org/search?q=$$
+    urlLabel ZFIN clone search:
+    searchIndex name
+    filterValues.concordant TRUE,FALSE
+    filterLabel.concordant End-pair concordance
+    filterType.concordant multipleListOnlyOr
+    filterValues.unique TRUE,FALSE
+    filterLabel.unique Unique placement
+    filterType.unique multipleListOnlyOr
+    filterValues.oversize TRUE,FALSE
+    filterLabel.oversize Oversize placement (>500kb)
+    filterType.oversize multipleListOnlyOr
+    skipFields score,strand,placementMethod
+    html choriCloneEnds
+
+searchTable choriCloneEndsCH73
+searchType bigBed
+searchPriority 20
+
+    track choriCloneEndsCH211
+    parent choriCloneEnds
+    shortLabel CHORI CH211
+    longLabel CHORI CH211 BAC library clone end placements, unique concordant
+    type bigBed 6 +
+    bigDataUrl /gbdb/danRer11/choriCloneEnds/CH211.bb
+    color 60,140,80
+    visibility pack
+    url https://zfin.org/search?q=$$
+    urlLabel ZFIN clone search:
+    searchIndex name
+    filterValues.concordant TRUE,FALSE
+    filterLabel.concordant End-pair concordance
+    filterType.concordant multipleListOnlyOr
+    filterValues.unique TRUE,FALSE
+    filterLabel.unique Unique placement
+    filterType.unique multipleListOnlyOr
+    filterValues.oversize TRUE,FALSE
+    filterLabel.oversize Oversize placement (>500kb)
+    filterType.oversize multipleListOnlyOr
+    skipFields score,strand,placementMethod
+    html choriCloneEnds
+
+searchTable choriCloneEndsCH211
+searchType bigBed
+searchPriority 20