cooler
Quickstart
What is cooler?
Concepts
Schema
API Reference
CLI Reference
Release notes
cooler
Index
Index
Symbols
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_
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A
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B
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C
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D
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E
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F
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I
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L
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M
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O
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P
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R
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S
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U
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Z
Symbols
--annotate
cooler-dump command line option
--append
cooler-cload-pairs command line option
cooler-coarsen command line option
cooler-load command line option
cooler-merge command line option
--assembly
cooler-cload-hiclib command line option
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-load command line option
--balance
cooler-zoomify command line option
--balance-args
cooler-zoomify command line option
--balanced
cooler-dump command line option
cooler-show command line option
--base-uri
cooler-zoomify command line option
--blacklist
cooler-balance command line option
--check
cooler-balance command line option
--chrom1
cooler-cload-pairs command line option
cooler-csort command line option
--chrom2
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
--chunksize
cooler-balance command line option
cooler-cload-hiclib command line option
cooler-cload-pairs command line option
cooler-coarsen command line option
cooler-dump command line option
cooler-load command line option
cooler-merge command line option
cooler-zoomify command line option
--cis-only
cooler-balance command line option
--cmap
cooler-show command line option
--columns
cooler-dump command line option
--comment-char
cooler-cload-pairs command line option
cooler-csort command line option
cooler-load command line option
--convergence-policy
cooler-balance command line option
--count-as-float
cooler-load command line option
--debug
cooler command line option
--dpi
cooler-show command line option
--factor
cooler-coarsen command line option
--field
cooler-cload-pairs command line option
cooler-coarsen command line option
cooler-info command line option
cooler-load command line option
cooler-merge command line option
cooler-show command line option
cooler-zoomify command line option
--fill-lower
cooler-dump command line option
--flip-only
cooler-csort command line option
--float-format
cooler-dump command line option
--force
cooler-balance command line option
cooler-show command line option
--format
cooler-load command line option
--header
cooler-digest command line option
cooler-dump command line option
cooler-makebins command line option
--ignore-diags
cooler-balance command line option
--ignore-dist
cooler-balance command line option
--index
cooler-csort command line option
--input-copy-status
cooler-cload-pairs command line option
cooler-load command line option
--join
cooler-dump command line option
--legacy
cooler-zoomify command line option
--level
cooler-attrs command line option
cooler-tree command line option
--long
cooler-ls command line option
--mad-max
cooler-balance command line option
--max-iters
cooler-balance command line option
--max-merge
cooler-cload-pairs command line option
--max-split
cooler-cload-pairix command line option
cooler-cload-tabix command line option
--metadata
cooler-cload-hiclib command line option
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-info command line option
cooler-load command line option
--min-count
cooler-balance command line option
--min-nnz
cooler-balance command line option
--na-rep
cooler-dump command line option
--name
cooler-balance command line option
--no-balance
cooler-dump command line option
--no-delete-temp
cooler-cload-pairs command line option
cooler-load command line option
--no-symmetric-upper
cooler-cload-pairs command line option
cooler-load command line option
--nproc
cooler-balance command line option
cooler-cload-pairix command line option
cooler-cload-tabix command line option
cooler-coarsen command line option
cooler-csort command line option
cooler-zoomify command line option
--one-based
cooler-load command line option
--one-based-ids
cooler-dump command line option
--one-based-starts
cooler-dump command line option
--out
cooler-coarsen command line option
cooler-csort command line option
cooler-digest command line option
cooler-dump command line option
cooler-info command line option
cooler-makebins command line option
cooler-show command line option
cooler-zoomify command line option
--overwrite
cooler-cp command line option
cooler-ln command line option
cooler-mv command line option
--pos1
cooler-cload-pairs command line option
cooler-csort command line option
--pos2
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
--range
cooler-dump command line option
--range2
cooler-dump command line option
cooler-show command line option
--rel-ids
cooler-digest command line option
cooler-makebins command line option
--resolutions
cooler-zoomify command line option
--scale
cooler-show command line option
--sep
cooler-csort command line option
--soft
cooler-ln command line option
--sort-options
cooler-csort command line option
--stdout
cooler-balance command line option
--storage-options
cooler-cload-pairs command line option
cooler-load command line option
--strand1
cooler-csort command line option
--strand2
cooler-csort command line option
--table
cooler-dump command line option
--temp-dir
cooler-cload-pairs command line option
cooler-load command line option
--tol
cooler-balance command line option
--trans-only
cooler-balance command line option
--verbose
cooler command line option
--version
cooler command line option
--zero-based
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
--zmax
cooler-show command line option
--zmin
cooler-show command line option
-0
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
-a
cooler-cload-pairs command line option
cooler-coarsen command line option
cooler-load command line option
cooler-merge command line option
-b
cooler-dump command line option
cooler-show command line option
-c
cooler-balance command line option
cooler-cload-hiclib command line option
cooler-coarsen command line option
cooler-dump command line option
cooler-load command line option
cooler-merge command line option
cooler-zoomify command line option
-c1
cooler-cload-pairs command line option
cooler-csort command line option
-c2
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
-d
cooler command line option
-f
cooler-balance command line option
cooler-dump command line option
cooler-info command line option
cooler-load command line option
cooler-show command line option
-H
cooler-digest command line option
cooler-dump command line option
cooler-makebins command line option
-i
cooler-csort command line option
cooler-digest command line option
cooler-makebins command line option
cooler-zoomify command line option
-k
cooler-coarsen command line option
cooler-dump command line option
-L
cooler-attrs command line option
cooler-tree command line option
-l
cooler-ls command line option
-m
cooler-info command line option
-N
cooler-cload-pairs command line option
cooler-load command line option
-n
cooler-coarsen command line option
cooler-zoomify command line option
-o
cooler-coarsen command line option
cooler-csort command line option
cooler-digest command line option
cooler-dump command line option
cooler-info command line option
cooler-makebins command line option
cooler-show command line option
cooler-zoomify command line option
-p
cooler-balance command line option
cooler-cload-pairix command line option
cooler-cload-tabix command line option
cooler-coarsen command line option
cooler-csort command line option
cooler-zoomify command line option
-p1
cooler-cload-pairs command line option
cooler-csort command line option
-p2
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
-r
cooler-dump command line option
cooler-zoomify command line option
-r2
cooler-dump command line option
cooler-show command line option
-s
cooler-cload-pairix command line option
cooler-cload-tabix command line option
cooler-ln command line option
cooler-show command line option
-s1
cooler-csort command line option
-s2
cooler-csort command line option
-t
cooler-dump command line option
-V
cooler command line option
-v
cooler command line option
-w
cooler-cp command line option
cooler-ln command line option
cooler-mv command line option
_
__init__() (cooler.Cooler method)
A
annotate() (in module cooler)
B
balance_cooler() (in module cooler)
binnify() (in module cooler.util)
BINS
cooler-cload-hiclib command line option
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
bins() (cooler.Cooler method)
BINS_PATH
cooler-load command line option
BINSIZE
cooler-makebins command line option
binsize (cooler.Cooler property)
C
chromnames (cooler.Cooler property)
CHROMOSOMES_PATH
cooler-csort command line option
chroms() (cooler.Cooler method)
chromsizes (cooler.Cooler property)
CHROMSIZES_PATH
cooler-digest command line option
cooler-makebins command line option
coarsen_cooler() (in module cooler)
COOL_PATH
cooler-balance command line option
cooler-cload-hiclib command line option
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-coarsen command line option
cooler-dump command line option
cooler-info command line option
cooler-load command line option
cooler-ls command line option
cooler-show command line option
cooler-zoomify command line option
Cooler (class in cooler)
cooler command line option
--debug
--verbose
--version
-d
-v
-V
cooler-attrs command line option
--level
-L
URI
cooler-balance command line option
--blacklist
--check
--chunksize
--cis-only
--convergence-policy
--force
--ignore-diags
--ignore-dist
--mad-max
--max-iters
--min-count
--min-nnz
--name
--nproc
--stdout
--tol
--trans-only
-c
-f
-p
COOL_PATH
cooler-cload-hiclib command line option
--assembly
--chunksize
--metadata
-c
BINS
COOL_PATH
PAIRS_PATH
cooler-cload-pairix command line option
--assembly
--max-split
--metadata
--nproc
--zero-based
-0
-p
-s
BINS
COOL_PATH
PAIRS_PATH
cooler-cload-pairs command line option
--append
--assembly
--chrom1
--chrom2
--chunksize
--comment-char
--field
--input-copy-status
--max-merge
--metadata
--no-delete-temp
--no-symmetric-upper
--pos1
--pos2
--storage-options
--temp-dir
--zero-based
-0
-a
-c1
-c2
-N
-p1
-p2
BINS
COOL_PATH
PAIRS_PATH
cooler-cload-tabix command line option
--assembly
--chrom2
--max-split
--metadata
--nproc
--pos2
--zero-based
-0
-c2
-p
-p2
-s
BINS
COOL_PATH
PAIRS_PATH
cooler-coarsen command line option
--append
--chunksize
--factor
--field
--nproc
--out
-a
-c
-k
-n
-o
-p
COOL_PATH
cooler-cp command line option
--overwrite
-w
DST_URI
SRC_URI
cooler-csort command line option
--chrom1
--chrom2
--comment-char
--flip-only
--index
--nproc
--out
--pos1
--pos2
--sep
--sort-options
--strand1
--strand2
--zero-based
-0
-c1
-c2
-i
-o
-p
-p1
-p2
-s1
-s2
CHROMOSOMES_PATH
PAIRS_PATH
cooler-digest command line option
--header
--out
--rel-ids
-H
-i
-o
CHROMSIZES_PATH
ENZYME
FASTA_PATH
cooler-dump command line option
--annotate
--balanced
--chunksize
--columns
--fill-lower
--float-format
--header
--join
--na-rep
--no-balance
--one-based-ids
--one-based-starts
--out
--range
--range2
--table
-b
-c
-f
-H
-k
-o
-r
-r2
-t
COOL_PATH
cooler-info command line option
--field
--metadata
--out
-f
-m
-o
COOL_PATH
cooler-ln command line option
--overwrite
--soft
-s
-w
DST_URI
SRC_URI
cooler-load command line option
--append
--assembly
--chunksize
--comment-char
--count-as-float
--field
--format
--input-copy-status
--metadata
--no-delete-temp
--no-symmetric-upper
--one-based
--storage-options
--temp-dir
-a
-c
-f
-N
BINS_PATH
COOL_PATH
PIXELS_PATH
cooler-ls command line option
--long
-l
COOL_PATH
cooler-makebins command line option
--header
--out
--rel-ids
-H
-i
-o
BINSIZE
CHROMSIZES_PATH
cooler-merge command line option
--append
--chunksize
--field
-a
-c
IN_PATHS
OUT_PATH
cooler-mv command line option
--overwrite
-w
DST_URI
SRC_URI
cooler-show command line option
--balanced
--cmap
--dpi
--field
--force
--out
--range2
--scale
--zmax
--zmin
-b
-f
-o
-r2
-s
COOL_PATH
RANGE
cooler-tree command line option
--level
-L
URI
cooler-zoomify command line option
--balance
--balance-args
--base-uri
--chunksize
--field
--legacy
--nproc
--out
--resolutions
-c
-i
-n
-o
-p
-r
COOL_PATH
cp() (in module cooler.fileops)
create_cooler() (in module cooler)
create_scool() (in module cooler)
D
digest() (in module cooler.util)
DST_URI
cooler-cp command line option
cooler-ln command line option
cooler-mv command line option
E
ENZYME
cooler-digest command line option
extent() (cooler.Cooler method)
F
FASTA_PATH
cooler-digest command line option
fetch_chromsizes() (in module cooler.util)
I
IN_PATHS
cooler-merge command line option
info (cooler.Cooler property)
is_cooler() (in module cooler.fileops)
is_multires_file() (in module cooler.fileops)
L
list_coolers() (in module cooler.fileops)
ln() (in module cooler.fileops)
M
matrix() (cooler.Cooler method)
merge_coolers() (in module cooler)
mv() (in module cooler.fileops)
O
offset() (cooler.Cooler method)
open() (cooler.Cooler method)
OUT_PATH
cooler-merge command line option
P
PAIRS_PATH
cooler-cload-hiclib command line option
cooler-cload-pairix command line option
cooler-cload-pairs command line option
cooler-cload-tabix command line option
cooler-csort command line option
partition() (in module cooler.util)
pixels() (cooler.Cooler method)
PIXELS_PATH
cooler-load command line option
R
RANGE
cooler-show command line option
read_chromsizes() (in module cooler.util)
rename_chroms() (in module cooler)
S
sanitize_pixels() (in module cooler.create)
sanitize_records() (in module cooler.create)
SRC_URI
cooler-cp command line option
cooler-ln command line option
cooler-mv command line option
storage_mode (cooler.Cooler property)
U
URI
cooler-attrs command line option
cooler-tree command line option
Z
zoomify_cooler() (in module cooler)