SYMBOL INDEX (21 symbols across 6 files)

FILE: bin/extract_map_reads.py
  function _get_args (line 14) | def _get_args():
  function extract_mapped (line 63) | def extract_mapped(bamfile, merged):
  function read_write_fq (line 92) | def read_write_fq(fq_in, fq_out, mapped_reads, mode, write_mode, proc):
  function check_remove_mode (line 130) | def check_remove_mode(mode):

FILE: bin/filter_bam_fragment_length.py
  function get_args (line 10) | def get_args():
  function getBasename (line 47) | def getBasename(file_name):
  function filter_bam (line 55) | def filter_bam(infile, outfile, fraglen, allreads):

FILE: bin/kraken_parse.py
  function _get_args (line 9) | def _get_args():
  function _get_basename (line 42) | def _get_basename(file_name):
  function parse_kraken (line 50) | def parse_kraken(infile, countlim):
  function write_output (line 79) | def write_output(resdict, infile, outfile):

FILE: bin/markdown_to_html.py
  function convert_markdown (line 10) | def convert_markdown(in_fn):
  function wrap_html (line 24) | def wrap_html(contents):
  function parse_args (line 74) | def parse_args(args=None):
  function main (line 83) | def main(args=None):

FILE: bin/merge_kraken_res.py
  function _get_args (line 11) | def _get_args():
  function get_csv (line 36) | def get_csv():
  function _get_basename (line 43) | def _get_basename(file_name):
  function merge_csv (line 51) | def merge_csv(all_csv):
  function write_csv (line 60) | def write_csv(pd_dataframe, outfile):

FILE: bin/print_x_contamination.py
  function make_float (line 13) | def make_float(x):