Just a few fixes

1. extract_all_discordants.sh 

a.Fixed flag checking that only requires a single thread
b.Cleans up tmp bams
c.Fixed a problem where the user specifies gte number of threads to the number of bams then causing the pipeline to jump ahead

2.make_hydra_config.py

a.Removed a deprecated function
b.Works on files in byte size descending order to most likely increase  runtimes