# 2026-04-21 Claude max

# Long-read SVs on hs1 (T2T-CHM13). HGSVC3 released a parallel set of SV
# annotation tables native to T2T-CHM13, which we convert with the same
# pipeline as the hg38 HGSVC3 subtrack. The full process (converter,
# autoSql, bigBed build, trackDb setup, summary table, references) is
# documented in ~/kent/src/hg/makeDb/doc/hg38/lrSv.txt; this file only
# lists the hs1-specific shell steps.

mkdir -p /hive/data/genomes/hs1/bed/lrSv/hgsvc3
cd /hive/data/genomes/hs1/bed/lrSv/hgsvc3

wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Variant_Calls/1.0/T2T-CHM13/annotation_table/variants_T2T-CHM13_sv_insdel_HGSVC2024v1.0.tsv.gz
wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Variant_Calls/1.0/T2T-CHM13/annotation_table/variants_T2T-CHM13_sv_inv_HGSVC2024v1.0.tsv.gz

# 188,224 DEL+INS + 276 INV = 188,500 SVs, natively on T2T-CHM13. The
# converter is the same one used for the hg38 track (shared .as + .py).
python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc3TsvToBed.py \
    variants_T2T-CHM13_sv_insdel_HGSVC2024v1.0.tsv.gz \
    variants_T2T-CHM13_sv_inv_HGSVC2024v1.0.tsv.gz \
    hgsvc3.bed
bedSort hgsvc3.bed hgsvc3.sorted.bed
bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as \
    -tab hgsvc3.sorted.bed /hive/data/genomes/hs1/chrom.sizes hgsvc3.bb

# Symlink under /gbdb/hs1/lrSv with the same filename as the hg38 track,
# so the trackDb bigDataUrl (/gbdb/$D/lrSv/hgsvc3.bb) resolves on both
# assemblies.
mkdir -p /gbdb/hs1/lrSv
ln -sf /hive/data/genomes/hs1/bed/lrSv/hgsvc3/hgsvc3.bb /gbdb/hs1/lrSv/hgsvc3.bb

##########
# 2026-04-21 Claude max
#
# OUTDATED, DO NOT RUN. The HPRC v2.0 wave track (hprc2Sv) was removed from
# trackDb on 2026-06-08 when the hg38 track moved to the v2.1 file
# (hprc2v21Sv, doc/hg38/lrSv.txt). The CHM13 v2.1 build is the next section
# below; this v2.0 recipe is kept, commented out, in case HPRC releases
# wave-decomposed VCFs again (the v2.0 converter handles their TYPE/LEN/INV
# fields, which the v2.1 raw deconstruct files do not have).
#
# # HPRC release-2 pangenome SVs on T2T-CHM13. HPRC releases one VCF per
# # reference path; we already have the GRCh38 version as the hprc2Sv
# # subtrack. The hs1 track is built from the parallel T2T-CHM13 wave VCF
# # with the same converter.
#
# mkdir -p /hive/data/genomes/hs1/bed/lrSv/hprc2
# cd /hive/data/genomes/hs1/bed/lrSv/hprc2
#
# aria2c -x10 https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-chm13.wave.vcf.gz
#
# python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2VcfToBed.py \
#     hprc-v2.0-mc-chm13.wave.vcf.gz hprc2.bed
# bedSort hprc2.bed hprc2.sorted.bed
# bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2.as \
#     -tab hprc2.sorted.bed /hive/data/genomes/hs1/chrom.sizes hprc2.bb
#
# ln -sf /hive/data/genomes/hs1/bed/lrSv/hprc2/hprc2.bb /gbdb/hs1/lrSv/hprc2.bb

##########
# 2026-06-09 Claude max

# hprc2v21Sv on T2T-CHM13: the CHM13 path of the HPRC v2.1 minigraph-cactus
# graph (233 samples). Same raw vg deconstruct file type as the hg38 v2.1
# build (no per-allele TYPE/LEN, graph traversals and nested snarls present),
# converted with the same parsimony-trimming converter. CHM13 contig names
# (chr1..chrY) already match the hs1 assembly, so no renaming is needed.

mkdir -p /hive/data/genomes/hs1/bed/lrSv/hprc2v21
cd /hive/data/genomes/hs1/bed/lrSv/hprc2v21

# VCF provided by Glenn Hickey (HPRC graph team):
wget https://public.gi.ucsc.edu/~ghickey/debug/hprc-v2.1-mc-chm13.gref95.ro.vcf.gz

python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2RoVcfToBed.py \
    hprc-v2.1-mc-chm13.gref95.ro.vcf.gz hprc2v21.bed
# kept 608435 SV-sized alleles: 363310 INS, 245125 DEL, 0 CPX
# (75809 at nested snarl levels LV>0)
bedSort hprc2v21.bed hprc2v21.sorted.bed
bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as \
    -tab hprc2v21.sorted.bed /hive/data/genomes/hs1/chrom.sizes hprc2v21.bb

##########
# 2026-06-13 Claude max
#
# QA fixes (refs #36258), hs1 side. See doc/hg38/lrSv.txt for the full writeup.
# The converters now drop byte-identical duplicate rows, so re-running the
# hs1 builds above gives the new counts:
#   hprc2v21 hs1  608,435 -> 541,176  (67,259 duplicates dropped)
# colorsDb hs1 and 1kgOnt hs1 were rebuilt from source for the shared color
# palette (CPX purple, colorsDb DEL 200,0,0); apr hs1 and cpc1 hs1 only needed
# the CPX color remapped, so their served bigBeds were recolored in place the
# same way as the hg38 files (see doc/hg38/lrSv.txt). There is no hs1 lrSvAll.
