.. _bam_example:

bam example
-----------
You can read more about preparing the files necessary for a bam track
on `UCSC's bam help page
<https://genome.ucsc.edu/goldenPath/help/bam.html>`_. The following code uses the example files provided by UCSC.

This code is automatically run and the built trackhub is uploaded to the
`trackhub-demo <https://github.com/daler/trackhub-demo>`_ repository. You can
view the live hub using `this link <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hubUrl=https://raw.githubusercontent.com/daler/trackhub-demo/master/example_bam_hub/bam.hub.txt&position=chr21:33038946-33039092>`_.

.. code-block:: python

    import trackhub

    hub, genomes_file, genome, trackdb = trackhub.default_hub(
        hub_name="bam",
        short_label="bam",
        long_label="bam",
        genome="hg18",
        defaultPos="chr21:33038946-33039092",
        email="eva.jason@nih.gov",
    )

    track = trackhub.Track(
        tracktype="bam",
        name="bam",
        description="bam ex. 1: 1000 genomes read alignments (individual na12878)",
        pairEndsByName=".",
        pairSearchRange="10000",
        chromosomes="chr21",
        maxWindowToDraw="200000",
        visibility="pack",
        bigDataUrl="http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam",
    )
    trackdb.add_tracks(track)
    trackhub.upload.upload_hub(
        hub=hub, host="localhost", remote_dir="example_hubs/example_bam_hub"
    )