Add ArchTEx Cross-Correlation analysis

[owlang]

ArchTEx cross-correlation analysis is useful for empirically determining tag shifts for ChIP-seq and other chromatin-digestion based assays for aligning forward and reverse tag alignments (e.g. performing combined TagPileup). Read more on tool Github/publication.

https://github.com/WilliamKMLai/ArchTEx

Currently can be executed by cloning the repo and running

cd ArchTEx
java -cp bin:sam-1.83.jar:jfreechart-1.0.13.jar:jcommon-1.0.16.jar gui.base.GUI

We want to port over the code from the repo and integrate it into ScriptManager to add command-line access and eventual integration with pipeline-development logging.

Notes on implementation:

• Add under BAM_Statistics
• Will need to redesign GUI to fit ScriptManager architecture
• bulk of script implementation is in ArchTEx.analysis.corr.CorrLoad
• update code to use current ScriptManager versions of JFree and HTSJDK
• determine custom object dependencies and create new scriptmanager.objects.ArchTEx package to organize them
  • may revisit object organization in the future
• go through New Tool checklist