qchar counts

qchar_count.py

try:
    from cytoolz import frequencies
except ImportError:
    from collections import Counter as frequencies
    # Works, but it's less than 3x as fast
    # A simple pure python counter is twice as fast as Counter anyhow....
from itertools import chain

def get_qchars_counts(bampath):
    '''
    Quickly gets you a distribution of quality scores.
    '''
    return frequencies(chain.from_iterable(c.qual for
                                           c in pysam.AlignmentFile(bampath)))