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# Copyright 2009-2015 CRS4.
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"""
Count the base frequency in sequencing data (in SAM format).

  input: file in SAM format
  output: tab-separated (base, count) pairs
"""


def mapper(_, samrecord, writer):
    seq = samrecord.split("\t", 10)[9]
    for c in seq:
        writer.emit(c, 1)
    writer.count("bases", len(seq))


def reducer(key, ivalue, writer):
    writer.emit(key, sum(map(int, ivalue)))
