text: # BEGIN_COPYRIGHT
  # 
  # Copyright 2009-2014 CRS4.
  # 
  # Licensed under the Apache License, Version 2.0 (the "License"); you may not
  # use this file except in compliance with the License. You may obtain a copy
  # of the License at
  # 
  #   http://www.apache.org/licenses/LICENSE-2.0
  # 
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
  # WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
  # License for the specific language governing permissions and limitations
  # under the License.
  # 
  # END_COPYRIGHT
  
  """
  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)))
  