Just a few fixes

General
============
Fixed some typos in command line parsers
Added frequency and run scripts
Added cleaning up
Added some parallelization and optimization


Detailed
============
1. extract_all_discordants.sh 

a.Fixed flag checking that only requires a single thread
b.Added a job queue with polling
c.Passes dataset names to add to bedpe query names

2.make_hydra_config.py

a.Removed a deprecated function
b.Works on files in byte size descending order to most likely decrease runtimes  

3.hydra.cpp

a.Reports the master route file in order of largest to smallest chr/chr/o/o to speed up runtimes
b.Cleans up leftover files from assembly
c.Added crumb mode

4.assemble-routed-files.sh

a.Added a job queue that polls

4.combined-assembled-files.sh

a.Added crumb mode
b.Cleans up old files

5.extract_discordants.py

a.Properly attaches dataset name to query(read) names

6.frequency.py

a.added this script and made the dataset check a bit more robust, now uses the same initial config file for hydra to map samples

7.hydra-multi.sh

a.added this script to run and test hydra-multi