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.. _api-reference:
API Reference
=============
.. toctree::
:maxdepth: 1
Quick reference
---------------
Cooler class
~~~~~~~~~~~~
.. autosummary::
cooler.Cooler
cooler.Cooler.binsize
cooler.Cooler.chromnames
cooler.Cooler.chromsizes
cooler.Cooler.bins
cooler.Cooler.pixels
cooler.Cooler.matrix
cooler.Cooler.open
cooler.Cooler.info
cooler.Cooler.offset
cooler.Cooler.extent
Creation/reduction
~~~~~~~~~~~~~~~~~~
.. autosummary::
cooler.create_cooler
cooler.merge_coolers
cooler.coarsen_cooler
cooler.zoomify_cooler
cooler.create_scool
Manipulation
~~~~~~~~~~~~
.. autosummary::
cooler.annotate
cooler.balance_cooler
cooler.rename_chroms
File operations
~~~~~~~~~~~~~~~
.. autosummary::
cooler.fileops.is_cooler
cooler.fileops.is_multires_file
cooler.fileops.list_coolers
cooler.fileops.cp
cooler.fileops.mv
cooler.fileops.ln
.. Sandbox
.. ~~~~~~~
.. .. autosummary::
.. cooler.sandbox.dask.read_table
----
cooler
------
.. autoclass:: cooler.Cooler
:members:
.. autofunction:: cooler.annotate
.. autofunction:: cooler.create_cooler
.. autofunction:: cooler.merge_coolers
.. autofunction:: cooler.coarsen_cooler
.. autofunction:: cooler.zoomify_cooler
.. autofunction:: cooler.balance_cooler
.. autofunction:: cooler.rename_chroms
.. autofunction:: cooler.create_scool
----
cooler.create
-------------
.. autofunction:: cooler.create.sanitize_pixels
.. autofunction:: cooler.create.sanitize_records
cooler.fileops
--------------
.. autofunction:: cooler.fileops.is_cooler
.. autofunction:: cooler.fileops.is_multires_file
.. autofunction:: cooler.fileops.list_coolers
.. autofunction:: cooler.fileops.cp
.. autofunction:: cooler.fileops.mv
.. autofunction:: cooler.fileops.ln
cooler.util
-----------
.. autofunction:: cooler.util.partition
.. autofunction:: cooler.util.fetch_chromsizes
.. autofunction:: cooler.util.read_chromsizes
.. autofunction:: cooler.util.binnify
.. autofunction:: cooler.util.digest
.. cooler.sandbox
.. --------------
.. .. autofunction:: cooler.sandbox.dask.read_table
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