streamline filenames

[nsheff]

sometimes we use periods, sometimes underscores, in a hodgepodge of files produced. let's standardize that (I vote all underscores) and streamline what's coming out of the pipeline.

Thoughts:

• How should we name wash_r2.pe.q10.sort.rmdup.bam? can we simplify?
• no need to include dual extensions in aligned_x_exact folder
• the unmap string should come after the genome in the filenames on prealignment outputs. that way each reference is grouped together in alphabetical order.
• can we just generally look through all output files and make sure their names are coherent?
• what is a .bamQC extension in the QC folder? it seems like a tsv or txt file.
• peaks/summits folders are named really nicely.

[jpsmith5]

See commit 27692faf87ed2bab6311c515cf84a3f9e642c14a.

• Switched over to underscores
• Reduced this to just *_sort_dedup.bam Used "dedup" nomenclature since we report that way.
• Changed the *.bw.bed to just *.bed
• Moved the unmap string as suggested
• Simplified the naming of several files to more directly reflect what they represent without getting overly wordy.
• Switched the bamQC over to just a .tsv which is what it is