diff --git a/docs_rst/config.rst b/docs_rst/config.rst index 7ddd352..ef72889 100644 --- a/docs_rst/config.rst +++ b/docs_rst/config.rst @@ -73,16 +73,16 @@ Each query can specify the following keys: - **direction**: Define the peak location relative to the feature's location, in respect of its orientation. A peak is 'upstream' if its center is upstream of a feature anchor position. Accordingly, a peak is 'downstream' if its center is downstream of a feature anchor position. - Also compare to Figure 2 in :doc:`/uropa-example`. + Visual repesentation in :ref:`Figure 1 ` of section :doc:`/uropa-example` Default: ``'any_direction'`` Example: ``'direction': ['upstream','downstream']`` - - Visual repesentation in :ref:`Figure 1 ` of section :doc:`/uropa-example` - - -- **internals**: This key represents a modifier with respect to the ``'distance'`` key. This can be helpful to annotate peaks to features with a wide size range, such as genes, which would otherwise be removed due to the distance thresholds. So even if the desired feature anchor is located too far away, a feature can still be included if it is overlapped. + +- **internals**: This key represents a modifier with respect to the ``'distance'`` key. + This can be helpful to annotate peaks to features with a wide size range, such as genes, + which would otherwise be removed due to the distance thresholds. So even if the desired feature anchor is located too far away, + a feature can still be included if it is overlapped. Visual repesentation in :ref:`Figure 1 ` of section :doc:`/uropa-example`. ``'center'``: If the center of a peak intersects with a feature region or vice versa, the ``'distance'`` key filtering is disabled. This parameter ensures that the majority of the peak intersects with the feature. @@ -100,7 +100,7 @@ Each query can specify the following keys: Example: ``'internals':'center'`` - Visual repesentation in :ref:`Figure 1 ` of section :doc:`/uropa-example` + - **filter.attribute** : Key filters the attributes found in the 9th column of the GTF file. If a ``'filter.attribute'`` is given, only features that have a ``'attribute.value'`` for this attribute is kept as valid annotations. If this key is set, the key ``'attribute.value'`` is mandatory, too (see below).