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/doc/danRer11/ncbiCloneEndsCH1073.txt src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt
deleted file mode 100644
index a8631027908..00000000000
--- src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-# NCBI CH1073 clone end placements track, refs #35059
-# 2026-04-21 Claude max
-
-mkdir -p /hive/data/genomes/danRer11/bed/ncbiCloneEndsCH1073
-cd /hive/data/genomes/danRer11/bed/ncbiCloneEndsCH1073
-
-# NCBI assembly report (has the UCSC-style name in column 10, so we just
-# project col 7 (RefSeq accession) onto col 10 (UCSC name))
-curl -sS -o GCF_000002035.6.assembly.txt \
-  'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_assembly_report.txt'
-
-# CH1073 unique_concordant placements (210777 clone_insert rows, ~48 MB)
-curl -sS -o CH1073.unique_concordant.gff \
-  'https://ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/CH1073.GCF_000002035.6.105.unique_concordant.gff'
-
-# RefSeq acc -> UCSC chrom name
-~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/refSeqNames.py \
-    GCF_000002035.6.assembly.txt > refSeq.ucscName.tab
-# 1923 mappings, all names present in /hive/data/genomes/danRer11/chrom.sizes
-
-# Parse GFF -> BED 6+7 (matches cloneEnds.as). All 210777 clone_insert rows
-# map to UCSC names; 26 are flagged as oversize (insertSize > 500 kb).
-~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/makeBed.py \
-    refSeq.ucscName.tab /hive/data/genomes/danRer11/chrom.sizes \
-    CH1073.unique_concordant.gff \
-    > ncbiCloneEndsCH1073.bed 2> makeBed.log
-
-# Sort and convert to bigBed
-sort -k1,1 -k2,2n ncbiCloneEndsCH1073.bed > ncbiCloneEndsCH1073.sorted.bed
-bedToBigBed -type=bed6+7 \
-    -as=~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as \
-    -tab ncbiCloneEndsCH1073.sorted.bed \
-    /hive/data/genomes/danRer11/chrom.sizes \
-    danRer11.ncbiCloneEndsCH1073.bb