maf-cut
=======

``maf-cut`` cuts out parts of MAF_ format alignments.  For example::

  maf-cut chr7:1234000-1235000 alignments.maf

This gets alignment parts within the range 1234000-1235000 of the
sequence named "chr7".  This is equivalent::

  maf-cut "chr7 1234000 1235000" alignments.maf

The ranges are zero-based.  For example, ``chr7:0-1000`` means the
first 1000 bases of chr7.

You can omit the sequence name::

  maf-cut 1234000-1235000 alignments.maf

Then, the range applies to the topmost sequence in each alignment.

``maf-cut`` can also get parts of sequences::

  maf-cut chr7:1234000-1235000 alignments.maf sequences.fasta

This first applies ``maf-cut`` to ``alignments.maf`` in the usual way
(without printing anything).  For each sequence, it gets the minimum
start coordinate and maximum end coordinate in the resulting
alignments.  It prints this segment of each sequence in
``sequences.fasta``.  (fastq format is ok too.)

.. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5
