.. seq:module:: bio.intervals

:seq:mod:`bio.intervals`
------------------------

Source code: `bio/intervals.seq <https://github.com/seq-lang/seq/blob/master/stdlib/bio/intervals.seq>`_

.. seq:class:: Interval

   **Properties:**

      .. seq:attribute:: start

      .. seq:attribute:: end

   **Magic methods:**

      .. seq:method:: __new__(st : int, en : int, chrom_id : int)
         :noindex:

      .. seq:method:: __len__()
         :noindex:

      .. seq:method:: __bool__()
         :noindex:

   **Methods:**

      .. seq:method:: with_max(max : int)



.. seq:class:: IntervalTree

   
       Interval tree data structure.
       Adapted from [cgranges](https://github.com/lh3/cgranges).
   

   **Magic methods:**

      .. seq:method:: __init__()
         :noindex:

      .. seq:method:: __len__()
         :noindex:

      .. seq:method:: __bool__()
         :noindex:

      .. seq:method:: __contains__(chrom : str)
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

            
                    Iterator over all intervals in the tree
            


   **Methods:**

      .. seq:method:: add(chrom : str, start : int, end : int)

            
                    Adds an interval to the tree. An interval is a chromosome name `chrom` and
                    0-based `start` and `end` (non-inclusive) positions.
            


      .. seq:method:: index()

            
                    Indexes the tree for querying.
            


      .. seq:method:: overlap(chrom : str, start : int, end : int)

            
                    Yields all `Interval`s overlapping the argument interval.