From 5b3a6d9cae61d3c3e53a6c86fe2d31e9923f7ee0 Mon Sep 17 00:00:00 2001 From: Annika Fust Date: Tue, 20 Jun 2017 13:27:16 +0200 Subject: [PATCH] updated internals flag manual --- docs_rst/config.rst | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/docs_rst/config.rst b/docs_rst/config.rst index be366bd..ad236bb 100644 --- a/docs_rst/config.rst +++ b/docs_rst/config.rst @@ -80,15 +80,21 @@ Each query can specify the following keys: Example: ``'direction': ['upstream','downstream']`` -- **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. - '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. + '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. - 'any': If a peak intersects with a feature region or vice versa, the ``'distance``' key filtering is disabled. An overlap of >= 1 nt is sufficient. + 'any': If a peak intersects with a feature region or vice versa, the ``'distance'`` key filtering is disabled. An overlap of >= 1 nt is sufficient. - Allowed values are one of ``'F', 'False', 'N', 'No'``, 'center', or 'any'. + 'none': Internals key is turned off. The ``'distance'`` key is active. - Default: ``'any'`` + Allowed values are one of ``'none', 'center', or 'any'.`` + + Furthermore, ``'T', 'True', 'Y', 'Yes'`` are allowed and will be treated as ``'center'``, + + ``'F', 'False', 'N', 'No'`` are allowed and will be treated as ``'none'``. + + Default: ``'none'`` Example: ``'internals':'center'``