.. raw:: html

    <a name="add-noise-configuration"></a>

.. _add-noise-configuration:

.. highlight:: none

.. parsed-literal::

    <:ref:`add-noise-configuration<add-noise-configuration>`> ::=
       {"input-h5" : <:ref:`file-name<file-name>`>,
        "output-h5" : <:ref:`file-name<file-name>`>,
        <:ref:`output-size-section<output-size-section>`>,
        "keep-original-data" : <:ref:`boolean<boolean>`>,
        "sequence-fraction-mutated" : <:ref:`number<number>`>,
        "sequence-distribution-fraction" : <:ref:`number<number>`>,
        "profile-mutation-types" : [<:ref:`list-of-profile-mutation-types<list-of-profile-mutation-types>`>],
        "num-threads" : <:ref:`integer<integer>`>,
        <:ref:`verbosity-section<verbosity-section>`>}
    
.. raw:: html

    <a name="output-size-section"></a>

.. _output-size-section:

.. highlight:: none

.. parsed-literal::

    <:ref:`output-size-section<output-size-section>`> ::=
        "num-output-samples" : <:ref:`integer<integer>`>
      | "output-size-ratio" : <:ref:`number<number>`>
    
.. raw:: html

    <a name="list-of-profile-mutation-types"></a>

.. _list-of-profile-mutation-types:

.. highlight:: none

.. parsed-literal::

    <:ref:`list-of-profile-mutation-types<list-of-profile-mutation-types>`> ::=
        <:ref:`profile-mutation-type<profile-mutation-type>`>
      | <:ref:`profile-mutation-type<profile-mutation-type>`>, <:ref:`list-of-profile-mutation-types<list-of-profile-mutation-types>`>
    
.. raw:: html

    <a name="profile-mutation-type"></a>

.. _profile-mutation-type:

.. highlight:: none

.. parsed-literal::

    <:ref:`profile-mutation-type<profile-mutation-type>`> ::=
        <:ref:`add-mutation-type<add-mutation-type>`>
      | <:ref:`shift-mutation-type<shift-mutation-type>`>
      | <:ref:`subtract-mutation-type<subtract-mutation-type>`>
    
.. raw:: html

    <a name="add-mutation-type"></a>

.. _add-mutation-type:

.. highlight:: none

.. parsed-literal::

    <:ref:`add-mutation-type<add-mutation-type>`> ::=
        {"type" : "add",
         "maximum-reads" : <:ref:`number-or-null<number-or-null>`>,
         "minimum-reads" : <:ref:`integer<integer>`>,
         "max-change" : <:ref:`integer<integer>`>,
         <:ref:`profile-mutation-common-parameters<profile-mutation-common-parameters>`>}
    
.. raw:: html

    <a name="shift-mutation-type"></a>

.. _shift-mutation-type:

.. highlight:: none

.. parsed-literal::

    <:ref:`shift-mutation-type<shift-mutation-type>`> ::=
        {"type" : "shift",
         "shift-max-distance" : <:ref:`integer<integer>`>,
         "shift-reads-independently" : <:ref:`boolean<boolean>`>,
         <:ref:`profile-mutation-common-parameters<profile-mutation-common-parameters>`>}
    
.. raw:: html

    <a name="subtract-mutation-type"></a>

.. _subtract-mutation-type:

.. highlight:: none

.. parsed-literal::

    <:ref:`subtract-mutation-type<subtract-mutation-type>`> ::=
        {"type" : "subtract",
         "maximum-reads" : <:ref:`number-or-null<number-or-null>`>,
         "minimum-reads" : <:ref:`integer<integer>`>,
         "max-change" : <:ref:`integer<integer>`>,
         <:ref:`profile-mutation-common-parameters<profile-mutation-common-parameters>`>}
    
.. raw:: html

    <a name="profile-mutation-common-parameters"></a>

.. _profile-mutation-common-parameters:

.. highlight:: none

.. parsed-literal::

    <:ref:`profile-mutation-common-parameters<profile-mutation-common-parameters>`> ::=
         "fraction-mutated" : <:ref:`number<number>`>,
         "output-distribution-fraction" : <:ref:`number<number>`>