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/scripts/ncbiCloneEndsCH1073/cloneEnds.as src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as
similarity index 89%
rename from src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as
rename to src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as
index 6e94ea01c0b..b1eb30e91f9 100644
--- src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as
+++ src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as
@@ -1,17 +1,17 @@
-table ncbiCloneEndsCH1073
-"NCBI CH1073 BAC library unique-concordant clone placements on danRer11"
+table choriCloneEnds
+"CHORI zebrafish BAC library unique-concordant clone placements (NCBI Clone DB)"
 (
 string  chrom;            "Reference sequence chromosome or scaffold"
 uint    chromStart;        "Start position (0-based)"
 uint    chromEnd;          "End position"
 string  name;              "Clone name (e.g. CH1073-100A1)"
 uint    score;             "Always 0 (not provided in source)"
 char[1] strand;            "Always + (not meaningful in source)"
 uint    insertSize;        "End - start of placement, bp"
 string  concordant;        "TRUE if this placement is concordant with the reference"
 string  unique;            "TRUE if this placement is unique in the genome"
 string  assmUnit;          "NCBI assembly unit (Primary Assembly, ALT_DRER_TU_1, etc.)"
 string  oversize;          "TRUE if insertSize > 500000|Flag for likely-spurious mappings"
 string  ncbiPlacementId;   "NCBI placement ID (GFF column-9 ID)"
 string  placementMethod;   "NCBI placement method (end-seq)"
 )