##
# varRep
##

track rmsk
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility hide
itemRgb on
type bigBed 9 +
bigDataUrl rmsk.bigBed
maxWindowToDraw 10000000
priority 1

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility hide
type bigBed 4 +
bigDataUrl trf.bigBed
priority 2

track as_annotation
shortLabel AS annotation
longLabel Alpha satellite annotation
group varRep
visibility hide
type bigBed 9
itemRgb on
bigDataUrl as_annotation.bigBed
maxItems 100000
priority 3

track hor_decompositions
shortLabel HOR annotation
longLabel Centromere HOR annotation
group varRep
visibility hide
itemRgb on
type bigBed 9
bigDataUrl hor_decompositions.bigBed
maxItems 100000
priority 4

# track segdups
# shortLabel Segmental Dups
# longLabel Segmental Duplications
# group varRep
# visibility hide
# itemRgb on
# type bigBed 9
# bigDataUrl segdups/segdups.bigBed
# priority 5

# track segdupslow
# shortLabel Segmental Dups Low Id
# longLabel Segmental Duplications Low Identity
# group varRep
# visibility hide
# itemRgb on
# type bigBed 9
# bigDataUrl segdups/segdupslow.bigBed
# html segdup.html
# priority 7

# track dupmasker
# shortLabel Ancestral Seg Dups
# longLabel Ancestral segmental duplications by DupMasker
# group varRep
# visibility hide
# itemRgb on
# type bigBed 9
# bigDataUrl dupmasker.bigBed
# priority 8




# # track merqury
# # shortLabel Merqury
# # longLabel Merqury
# # superTrack on hide
# # visibility hide
# # group map
# # priority 10

#     track merqury_10X_reads_kmers
#     #parent merqury
#     shortLabel Merqury 10XG k-mers
#     longLabel Merqury k-mer multiplicity in 10XG reads
#     type bigWig 0.0 100.0
#     color 60,60,140
#     altColor 140,60,60
#     visibility hide
#     bigDataUrl merqury/merqury_10X_reads_kmers.bigWig
#     viewLimitsMax 0:100
#     maxHeightPixels 100:32:8
#     priority 1
#     group map

#     track merqury_assembly_kmers
#     #parent merqury
#     shortLabel Merqury assembly k-mers
#     longLabel Merqury k-mer multiplicity in assembly
#     color 60,60,140
#     altColor 140,60,60
#     type bigWig 0.0 100.0
#     visibility hide
#     bigDataUrl merqury/merqury_assembly_kmers.bigWig
#     viewLimitsMax 0:100
#     maxHeightPixels 100:32:8
#     priority 2
#     group map

#     track merqury_marker_kmers
#     #parent merqury
#     shortLabel Merqury marker k-mers
#     longLabel Merqury Single copy marker k-mers
#     color 60,60,140
#     altColor 140,60,60
#     type bigWig 0.0 100.0
#     visibility hide
#     bigDataUrl merqury/merqury_marker_kmers.bigWig
#     viewLimitsMax 0:100
#     maxHeightPixels 100:32:8
#     priority 3
#     group map

#     track merqury_errors
#     #parent merqury
#     shortLabel Merqury errors
#     longLabel Merqury - Assembly-only (Errors)
#     color 60,60,140
#     altColor 140,60,60
#     type bigWig 0.0 100.0
#     visibility hide
#     bigDataUrl merqury/merqury_errors.bigWig
#     viewLimitsMax 0:100
#     maxHeightPixels 100:32:8
#     priority 4
#     group map

# # track winnowmap_nanopore
# # shortLabel Winnowmap Nanopore SVs
# # longLabel Winnowmap Nanopore SVs
# # superTrack on hide
# # visibility hide
# # group map
# # priority 10

#     track winnowmap_nanopore_aligns
#     #parent winnowmap_nanopore
#     shortLabel Winnowmap Nanopore Alignments
#     longLabel Winnowmap Nanopore Alignments
#     priority 10
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl winnowmap_nanopore/winnowmap_nanopore_aligns.bam
#     group map

#     track winnowmap_nanopore_variants
#     #parent winnowmap_nanopore
#     shortLabel Winnowmap Nanopore Variants
#     longLabel  Winnowmap Nanopore Variants
#     type vcfTabix
#     maxWindowToDraw 200000
#     bigDataUrl winnowmap_nanopore/winnowmap_nanopore_variants.vcf.gz
#     priority 20
#     visibility hide
#     group map

# # track hg002_aligns
# # shortLabel HG002 to CHM13 alignments
# # longLabel HG002 to CHM13 alignments
# # superTrack on hide
# # visibility hide
# # group compGeno
# # priority 10

#     track HG002vCHM13_20200602_mm2_ONT
#     #parent hg002_aligns
#     shortLabel HG002 ONT minimap2
#     longLabel HG002 ONT minimap2 alignments
#     priority 10
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_ONT.sort.bam
#     group compGeno

#     track HG002vCHM13_20200602_mm2_PBCCS
#     #parent hg002_aligns
#     shortLabel HG002 PacBio HiFi minimap2
#     longLabel HG002 PacBio HiFi minimap2 alignments
#     priority 11
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_PBCCS.sort.bam
#     group compGeno

#     track HG002vCHM13_20200602_mm2_PB
#     #parent hg002_aligns
#     shortLabel HG002 PacBio CLR minimap2
#     longLabel HG002 PacBio CLR minimap2 alignments
#     priority 12
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_PB.sort.bam
#     group compGeno

#     track HG002vCHM13_20200602_ngmlr_PBCCS
#     #parent hg002_aligns
#     shortLabel HG002 PacBio HiFi NGMLR
#     longLabel HG002 PacBio HiFi NGMLR alignments
#     priority 13
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl HG002vCHM13/HG002vCHM13_20200602_ngmlr_PBCCS.sort.bam
#     group compGeno

#     track HG002vCHM13_20200602_ngmlr_PB
#     #parent hg002_aligns
#     shortLabel HG002 PacBio CLR NGMLR
#     longLabel HG002 PacBio CLR NGMLR alignments
#     priority 14
#     type bam
#     maxItems 1000000
#     visibility hide
#     bigDataUrl HG002vCHM13/HG002vCHM13_20200602_ngmlr_PB.sort.bam
#     group compGeno