# Path: mitty/lib/sanitizeseq.py
# def sanitize(seq):
#   return seq.translate(sanitable)
# 
# 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)))


import time
import pysam
import numpy as np
import mitty.lib.vcfio as vio
import mitty.simulation.rpc as rpc
import logging
from multiprocessing import Process, Queue
from mitty.lib.sanitizeseq import sanitize
from mitty.simulation.sequencing.writefastq import writer
  :param truncate_to: If set, shorten reads to this length
  :param unpair: If True, for models that produce paired-end reads, produce single end, instead
  :param threads:
  :param seed:
  :return:
  """
  if truncate_to is not None:
    model['mean_rlen'] = min(truncate_to, model['mean_rlen'])
    logger.debug('Truncating mean read length to: {}bp'.format(model['mean_rlen']))
  if unpair:
    logger.debug('Un-pairing reads')
    model['unpaired'] = True
    assert fastq2_fname is None, 'For unpaired reads, no FASTQ2 should be supplied'
  read_model = read_module.read_model_params(model, coverage)

  global vcf_df
  vcf_df = vio.load_variant_file(vcf_fname, sample_name, bed_fname)

  in_queue = Queue()
  out_queue = Queue(10000)  # This is the key to preventing workers from dying

  logger.debug('Starting {} workers'.format(threads))
  workers = []
  for worker_id in range(threads):
    p = Process(target=read_generating_worker,
                args=(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue))
    p.start()
    workers.append(p)

  logger.debug('Starting writer process')

# Path: mitty/lib/sanitizeseq.py
# def sanitize(seq):
#   return seq.translate(sanitable)
# 
# 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)))


# Path: mitty/simulation/readgenerate.py
import time
import pysam
import numpy as np
import mitty.lib.vcfio as vio
import mitty.simulation.rpc as rpc
import logging
from multiprocessing import Process, Queue
from mitty.lib.sanitizeseq import sanitize
from mitty.simulation.sequencing.writefastq import writer

  :param truncate_to: If set, shorten reads to this length
  :param unpair: If True, for models that produce paired-end reads, produce single end, instead
  :param threads:
  :param seed:
  :return:
  """
  if truncate_to is not None:
    model['mean_rlen'] = min(truncate_to, model['mean_rlen'])
    logger.debug('Truncating mean read length to: {}bp'.format(model['mean_rlen']))
  if unpair:
    logger.debug('Un-pairing reads')
    model['unpaired'] = True
    assert fastq2_fname is None, 'For unpaired reads, no FASTQ2 should be supplied'
  read_model = read_module.read_model_params(model, coverage)

  global vcf_df
  vcf_df = vio.load_variant_file(vcf_fname, sample_name, bed_fname)

  in_queue = Queue()
  out_queue = Queue(10000)  # This is the key to preventing workers from dying

  logger.debug('Starting {} workers'.format(threads))
  workers = []
  for worker_id in range(threads):
    p = Process(target=read_generating_worker,
                args=(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue))
    p.start()
    workers.append(p)

  logger.debug('Starting writer process')

  wr = Process(target=writer, args=(fastq1_fname, sidecar_fname, fastq2_fname, out_queue))