this is a stripped down set of classes to implement a basic NGS analysis pipeline
This is allows the stepwise analysis of an NGS dataset. Output from one step serves as input to the subsequent step, 
so the analysis needs to follow a logical order. 
For example, mapping must come before read counting, and adapter trimming must precede mapping.

Basic command line execution is as follows:

java -jar -Dlog4j.configurationFile=file:log4j2.xml  NGSsmallRNA.jar -r configuration.yaml -p pipeline.json -d ngsdata.tsv

where the yaml file contains parameters for each step, the json file specifies which steps should be performed, 
and the tsv file specifies the data to be analyzed

An analysis step is derived from two base classes, NGSStep.java and NGSBase.java. This ensures consistency across all steps