Multiprocessing using process instead of pool

[theottlo]

1. Fixed simulation of perfect reads in transcriptome mode

   • New file is created in head_align_tail_dist.py: aligned_reads_2d.pkl
   • If per and in transcriptome mode, this file is read in simulation.read_profile

2. Minor changes to simulator.py

   • Fixed alignment in simulation
   • Used appropriate variable in simulation_aligned_transcriptome