# 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
  np.random.RandomState(shuffle_seed).shuffle(region_list)

  for region in region_list:
    yield region


# def read_generating_worker(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue):
#   for ps, wd in enumerate(iter(in_queue.get, __process_stop_code__)):
#     out_queue.put([str(ps), str(wd)])


def read_generating_worker(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue):
  """This worker will be given a fasta_fname, and region information. It is to generate the node_list,
  the read locations and then, finally, the reads themselves. The reads - in FASTQ format - are returned
  to the parent thread for writing.

  :param worker_id: Just a serial that helps us number reads uniquely
  :param fasta_fname:
  :param sample_name:  (This is just passed to the read qname)
  :param model:
  :param region_idx:
  :param in_queue: will be sending work information as (region_idx, cpy)
  :param out_queue: We'll be sending strings representing each template in FASTQ format
  :return:
  """
  fasta = pysam.FastaFile(fasta_fname)
  total_cnt, t00 = 0, time.time()
  for ps, wd in enumerate(iter(in_queue.get, __process_stop_code__)):
    r_idx, cpy, rng_seed = wd['region_idx'], wd['region_cpy'], wd['rng_seed']
    region = vcf_df[r_idx]['region']

# 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

  np.random.RandomState(shuffle_seed).shuffle(region_list)

  for region in region_list:
    yield region


# def read_generating_worker(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue):
#   for ps, wd in enumerate(iter(in_queue.get, __process_stop_code__)):
#     out_queue.put([str(ps), str(wd)])


def read_generating_worker(worker_id, fasta_fname, sample_name, read_module, read_model, in_queue, out_queue):
  """This worker will be given a fasta_fname, and region information. It is to generate the node_list,
  the read locations and then, finally, the reads themselves. The reads - in FASTQ format - are returned
  to the parent thread for writing.

  :param worker_id: Just a serial that helps us number reads uniquely
  :param fasta_fname:
  :param sample_name:  (This is just passed to the read qname)
  :param model:
  :param region_idx:
  :param in_queue: will be sending work information as (region_idx, cpy)
  :param out_queue: We'll be sending strings representing each template in FASTQ format
  :return:
  """
  fasta = pysam.FastaFile(fasta_fname)
  total_cnt, t00 = 0, time.time()
  for ps, wd in enumerate(iter(in_queue.get, __process_stop_code__)):
    r_idx, cpy, rng_seed = wd['region_idx'], wd['region_cpy'], wd['rng_seed']
    region = vcf_df[r_idx]['region']

    ref_seq = sanitize(fasta.fetch(reference=region[0], start=region[1], end=region[2]))