Bedtools CRAM support

[eugenegardner]

It appears that pybedtools does not support cram at the moment since it was added to bedtools in version 2.28 this past May. This mainly appears due to:

1. Some bedtools requiring the -ibam flag instead of the -i flag and
2. pybedtools checking only for the bam magic number when deciding whether to use the -ibam flag or not.

This can be seen in the code snippet of helpers.py:

def isBAM(fn):
    """
    Returns True if the file is both BGZIPed and the compressed contents have
    start with the magic number `BAM\\x01`.
    """
    # Note: previously we were catching ValueError when trying to open
    # a non-BAM with pysam.Samfile. That started segfaulting, so now do it the
    # right way with magic number.
    if isBGZIP(fn) and (gzip.open(fn, 'rb').read(4).decode() == 'BAM\x01'):
        return True

You can backdoor this functionality by doing something like:

bt = bedtools.BedTool(self.input_bam)
bt._isbam = True
bg_file = bt.genome_coverage(bg=True)

But this feels like bad coding practice. Figured it's reasonably quick fix to check for the CRAM magic number as well?