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afust committed Sep 13, 2017
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Expand Up @@ -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 <genomic-location>` of section :doc:`/uropa-example`

Default: ``'any_direction'``

Example: ``'direction': ['upstream','downstream']``

Visual repesentation in :ref:`Figure 1 <genomic-location>` 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 <genomic-location>` 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.

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Example: ``'internals':'center'``

Visual repesentation in :ref:`Figure 1 <genomic-location>` 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).
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