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link to visual representation
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afust committed Sep 13, 2017
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Expand Up @@ -78,6 +78,8 @@ Each query can specify the following keys:
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.
Expand All @@ -98,6 +100,7 @@ Each query can specify the following keys:

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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