Local BAM files

[manzt]

BAM Files
---------

View sequencing read mappings. First we must load the `higlass-pileup plugin track <https://github.com/higlass/higlass-pileup>`_
as a ``hg.PluginTrack``:



.. code-block:: python

	%%javascript

	require(["https://unpkg.com/higlass-pileup/dist/higlass-pileup.min.js"],
	    function(hglib) {

	});

And then we can view pileups:

.. code-block:: python

	import higlass
	from higlass.tilesets import Tileset, bam
	from higlass.client import Track, View

	filename = '../data/ont.10K.bam'
	indexfile = '../data/ont.10K.bam.bai'

	bam_ts = bam(filename, indexfile)

	display, server, viewconf = higlass.display(
	    [View([
	        Track('top-axis', height=20),
	        Track(track_type="pileup",
	        	position='top', tileset=bam_ts, height=50 )
	    ], initialXDomain = [
	        0,
	        2000
	      ])]
	)
	display

.. image:: img/jupyter-pileup-no-code.png

Usage of the BAM files is shown in the plugin documentation, but we don't currently support local files and would need to extend the server.

[manzt]

@nvictus maybe an oxbow use case