Retrieve alignment stats from picard using BamIndexStats.

def picard_idxstats(picard, align_bam):
    """Retrieve alignment stats from picard using BamIndexStats.
    """
    opts = [("INPUT", align_bam)]
    stdout = picard.run("BamIndexStats", opts, get_stdout=True)
    out = []
    AlignInfo = collections.namedtuple("AlignInfo", ["contig", "length", "aligned", "unaligned"])
    for line in stdout.split("\n"):
        if line:
            parts = line.split()
            if len(parts) == 2:
                _, unaligned = parts
                out.append(AlignInfo("nocontig", 0, 0, int(unaligned)))
            elif len(parts) == 7:
                contig, _, length, _, aligned, _, unaligned = parts
                out.append(AlignInfo(contig, int(length), int(aligned), int(unaligned)))
            else:
                raise ValueError("Unexpected output from BamIndexStats: %s" % line)
    return out