# Path: ariba/common.py
# class Error (Exception): pass
# def syscall(cmd, allow_fail=False, verbose=False, verbose_filehandle=sys.stdout, print_errors=True, shell=True):
# def decode(x):
# def cat_files(infiles, outfile):
# def download_file(url, outfile, max_attempts=3, sleep_time=2, verbose=False):
# def rmtree(input_dir):
# 
# Path: ariba/external_progs.py
# class Error (Exception): pass
# class ExternalProgs:
#     def __init__(self, verbose=False, fail_on_error=True, using_spades=False):
#     def exe(self, prog):
#     def version(self, prog):
#     def _get_exe(prog):
#     def _get_version(prog, path):


import os
import tempfile
from ariba import common, external_progs


class Error (Exception): pass

class ReadFilter:
    def __init__(self,
        readstore_obj,

# Path: ariba/common.py
# class Error (Exception): pass
# def syscall(cmd, allow_fail=False, verbose=False, verbose_filehandle=sys.stdout, print_errors=True, shell=True):
# def decode(x):
# def cat_files(infiles, outfile):
# def download_file(url, outfile, max_attempts=3, sleep_time=2, verbose=False):
# def rmtree(input_dir):
# 
# Path: ariba/external_progs.py
# class Error (Exception): pass
# class ExternalProgs:
#     def __init__(self, verbose=False, fail_on_error=True, using_spades=False):
#     def exe(self, prog):
#     def version(self, prog):
#     def _get_exe(prog):
#     def _get_version(prog, path):


# Path: ariba/read_filter.py
import os
import tempfile
from ariba import common, external_progs



class Error (Exception): pass

class ReadFilter:
    def __init__(self,
        readstore_obj,

        references_fa,