# Path: mitty/simulation/sequencing/writefastq.py
# def writer(fastq1_out, side_car_out, fastq2_out=None, data_queue=None, max_qname_len=__max_qname_len__):
#   """Write templates to file
# 
#   :param fastq1_out: Name of FASTQ1
#   :param side_car_out: Name of side car file for long qnames
#   :param fastq2_out: If paired end, name of FASTQ2
#   :param data_queue: multiprocessing queue
#   :param max_qname_len: Send qnames longer than this to the overflow file
# 
#     The data format is as follows:
#       (
#         idx,  - if this is None then we create an index afresh
#         sample_name,
#         chrom,
#         copy,
#         (
#           (strand, pos, cigar, (v1,v2,...), MD, seq, qual)
#         ...  [repeated as for as many reads in this template]
#         )
#       )
# 
#   :return:
#   """
#   t0 = time.time()
# 
#   cnt = -1
#   fastq_l, side_car_fp = [open(fastq1_out, 'w')], open(side_car_out, 'w')
#   if fastq2_out is not None: fastq_l += [open(fastq2_out, 'w')]
#   for cnt, template in enumerate(iter(data_queue.get, __process_stop_code__)):
#     # @index|sn|chrom:copy|
#     qname = '@{}|{}|{}:{}|'.format(template[0] or base_repr(cnt, 36), *template[1:4])
#     # strand:pos:cigar:v1,v2,...:MD|strand:pos:cigar:v1,v2,...:MD*
#     qname += '|'.join('{}:{}:{}:{}:{}'.format(*r[:3], str(r[3])[1:-1].replace(' ', ''), r[4]) for r in template[4]) + '*'
# 
#     if len(qname) > max_qname_len:
#       side_car_fp.write(qname + '\n')
#       qname = qname[:max_qname_len]
# 
#     for fp, r in zip(fastq_l, template[4]):
#       fp.write('{}\n{}\n+\n{}\n'.format(qname, r[5], r[6]))
# 
#   for fp in fastq_l:
#     fp.close()
# 
#   t1 = time.time()
#   logger.debug('Writer finished: {} templates in {:0.2f}s ({:0.2f} t/s)'.format(cnt + 1, t1 - t0, (cnt + 1) / (t1 - t0)))
# 
# def load_qname_sidecar(sidecar_fn):
#   def parse_sidecar_file(_fn):
#     with open(_fn, 'r') as fp:
#       for ln in fp:
#         yield ln.split('|', 1)[0][1:], ln[1:-1]
#   return {
#     k: v
#     for k, v in parse_sidecar_file(sidecar_fn)
#   }
# 
# def parse_qname(qname, long_qname_table=None):
#   """Given a Mitty qname return us the POS and CIGAR as we would put in a BAM. There is also a special_cigar
#   which is set for reads completely inside long insertions
# 
#   @index|sn|chrom:copy|strand:pos:cigar:v1,v2,...:MD|strand:pos:cigar:v1,v2,...:MD*
# 
#   :param qname:
#   :param long_qname_table: If present, is a map of qname index and qname for just the long qnames
#   :return: pos, cigar, special_cigar
#   """
#   def _parse_(_cigar, _v_list):
#     """
#     Parse cigar to extract special_cigar if needed
#     Parse v_list
# 
#     :param _cigar:
#     :param _v_list:
#     :return:
#     """
#     if _cigar[0] == '>':  # This is a special_cigar for a read from inside an insertion
#       _special_cigar = _cigar
#       _cigar = _cigar.split('+')[-1]
#     else:
#       _special_cigar = None
# 
#     return _cigar, _special_cigar, [int(v) for v in _v_list.split(',') if v is not '']
# 
#   def _split_(_r):
#     strand, pos, cigar, v_list, md = _r.split(':')
#     return (int(strand), int(pos)) + _parse_(cigar, v_list) + (md,)
# 
#   if qname[-1] != '*':  # Truncated qname
#     if long_qname_table is None:
#       raise ValueError('Long qname with no table lookup')  # It's the caller's responsibility to handle this error
#     _qname = long_qname_table.get(qname.split('|', 1)[0], None)
#     if _qname is None:
#       raise ValueError('Long qname with no table lookup: {}, {}'.format(qname.split('|', 1)[0], qname))
#       # It's the caller's responsibility to handle this error
#     qname = _qname
# 
#   d = qname[:-1].split('|')  # Strip out the terminal '*'
#   serial, sample = d[:2]
#   chrom, cpy = d[2].split(':')
#   cpy = int(cpy)
#   return [
#     ri(serial, sample, chrom, cpy, *_split_(r))
#     for r in d[3:]
#   ]


from multiprocessing import Process, Queue
from mitty.simulation.sequencing.writefastq import writer, load_qname_sidecar, parse_qname
import time
import pysam
import numpy as np
import logging
"""Contains the logic for handling read model corruption invocation"""



logger = logging.getLogger(__name__)


SEED_MAX = (1 << 32) - 1  # Used for seeding rng
__process_stop_code__ = 'SETECASTRONOMY'


def multi_process(read_module, read_model, fastq1_in, fastq1_out, sidecar_in, sidecar_out,
                  fastq2_in=None, fastq2_out=None, processes=2, seed=7):
  """

  :param read_module:
  :param read_model:
  :param fastq1_in:
  :param fastq1_out:
  :param sidecar_in:
  :param sidecar_out:
  :param fastq2_in:
  :param fastq2_out:
  :param processes:
  :param seed:
  :return:
  """


# Path: mitty/simulation/sequencing/writefastq.py
# def writer(fastq1_out, side_car_out, fastq2_out=None, data_queue=None, max_qname_len=__max_qname_len__):
#   """Write templates to file
# 
#   :param fastq1_out: Name of FASTQ1
#   :param side_car_out: Name of side car file for long qnames
#   :param fastq2_out: If paired end, name of FASTQ2
#   :param data_queue: multiprocessing queue
#   :param max_qname_len: Send qnames longer than this to the overflow file
# 
#     The data format is as follows:
#       (
#         idx,  - if this is None then we create an index afresh
#         sample_name,
#         chrom,
#         copy,
#         (
#           (strand, pos, cigar, (v1,v2,...), MD, seq, qual)
#         ...  [repeated as for as many reads in this template]
#         )
#       )
# 
#   :return:
#   """
#   t0 = time.time()
# 
#   cnt = -1
#   fastq_l, side_car_fp = [open(fastq1_out, 'w')], open(side_car_out, 'w')
#   if fastq2_out is not None: fastq_l += [open(fastq2_out, 'w')]
#   for cnt, template in enumerate(iter(data_queue.get, __process_stop_code__)):
#     # @index|sn|chrom:copy|
#     qname = '@{}|{}|{}:{}|'.format(template[0] or base_repr(cnt, 36), *template[1:4])
#     # strand:pos:cigar:v1,v2,...:MD|strand:pos:cigar:v1,v2,...:MD*
#     qname += '|'.join('{}:{}:{}:{}:{}'.format(*r[:3], str(r[3])[1:-1].replace(' ', ''), r[4]) for r in template[4]) + '*'
# 
#     if len(qname) > max_qname_len:
#       side_car_fp.write(qname + '\n')
#       qname = qname[:max_qname_len]
# 
#     for fp, r in zip(fastq_l, template[4]):
#       fp.write('{}\n{}\n+\n{}\n'.format(qname, r[5], r[6]))
# 
#   for fp in fastq_l:
#     fp.close()
# 
#   t1 = time.time()
#   logger.debug('Writer finished: {} templates in {:0.2f}s ({:0.2f} t/s)'.format(cnt + 1, t1 - t0, (cnt + 1) / (t1 - t0)))
# 
# def load_qname_sidecar(sidecar_fn):
#   def parse_sidecar_file(_fn):
#     with open(_fn, 'r') as fp:
#       for ln in fp:
#         yield ln.split('|', 1)[0][1:], ln[1:-1]
#   return {
#     k: v
#     for k, v in parse_sidecar_file(sidecar_fn)
#   }
# 
# def parse_qname(qname, long_qname_table=None):
#   """Given a Mitty qname return us the POS and CIGAR as we would put in a BAM. There is also a special_cigar
#   which is set for reads completely inside long insertions
# 
#   @index|sn|chrom:copy|strand:pos:cigar:v1,v2,...:MD|strand:pos:cigar:v1,v2,...:MD*
# 
#   :param qname:
#   :param long_qname_table: If present, is a map of qname index and qname for just the long qnames
#   :return: pos, cigar, special_cigar
#   """
#   def _parse_(_cigar, _v_list):
#     """
#     Parse cigar to extract special_cigar if needed
#     Parse v_list
# 
#     :param _cigar:
#     :param _v_list:
#     :return:
#     """
#     if _cigar[0] == '>':  # This is a special_cigar for a read from inside an insertion
#       _special_cigar = _cigar
#       _cigar = _cigar.split('+')[-1]
#     else:
#       _special_cigar = None
# 
#     return _cigar, _special_cigar, [int(v) for v in _v_list.split(',') if v is not '']
# 
#   def _split_(_r):
#     strand, pos, cigar, v_list, md = _r.split(':')
#     return (int(strand), int(pos)) + _parse_(cigar, v_list) + (md,)
# 
#   if qname[-1] != '*':  # Truncated qname
#     if long_qname_table is None:
#       raise ValueError('Long qname with no table lookup')  # It's the caller's responsibility to handle this error
#     _qname = long_qname_table.get(qname.split('|', 1)[0], None)
#     if _qname is None:
#       raise ValueError('Long qname with no table lookup: {}, {}'.format(qname.split('|', 1)[0], qname))
#       # It's the caller's responsibility to handle this error
#     qname = _qname
# 
#   d = qname[:-1].split('|')  # Strip out the terminal '*'
#   serial, sample = d[:2]
#   chrom, cpy = d[2].split(':')
#   cpy = int(cpy)
#   return [
#     ri(serial, sample, chrom, cpy, *_split_(r))
#     for r in d[3:]
#   ]


# Path: mitty/simulation/readcorrupt.py
from multiprocessing import Process, Queue
from mitty.simulation.sequencing.writefastq import writer, load_qname_sidecar, parse_qname
import time
import pysam
import numpy as np
import logging

"""Contains the logic for handling read model corruption invocation"""



logger = logging.getLogger(__name__)


SEED_MAX = (1 << 32) - 1  # Used for seeding rng
__process_stop_code__ = 'SETECASTRONOMY'


def multi_process(read_module, read_model, fastq1_in, fastq1_out, sidecar_in, sidecar_out,
                  fastq2_in=None, fastq2_out=None, processes=2, seed=7):
  """

  :param read_module:
  :param read_model:
  :param fastq1_in:
  :param fastq1_out:
  :param sidecar_in:
  :param sidecar_out:
  :param fastq2_in:
  :param fastq2_out:
  :param processes:
  :param seed:
  :return:
  """


  long_qname_table = load_qname_sidecar(sidecar_in)