===== Usage ===== Streaming Pileupy is meant to be run through its command line interface ``spileup``. Given a sam file ``in.sam``: .. code-block:: text @HD VN:1.6 SO:unknown @SQ SN:chr1 LN:1000000 @RG ID:0 SM:sample_0 @RG ID:1 SM:sample_1 r0 0 chr1 24 0 1M * 0 0 G I RG:Z:0 r1 0 chr1 24 0 1M * 0 0 G I RG:Z:1 , and a sample name file ``sample_names.txt``: .. code-block:: text sample_0 sample_1 To run a pileup of the reads in ``in.sam`` for the samples in ``sample_names.txt``, run the command: .. code-block:: bash spileup input.sam sample_names.txt