reimplement CLI (in progress)

src/main/java/CommandLineInterface.java

@@ -1,6 +1,45 @@
 import org.apache.commons.cli.*;
 
-//Class for parsing options passed to program from command line
+/*
+ * Class for parsing options passed to program from command line
+ *
+ * Top-level flags:
+ * cells : to make a cell sample file
+ * plate : to make a sample plate file
+ * graph : to make a graph and data file
+ * match : to do a cdr3 matching (WITH OR WITHOUT MAKING A RESULTS FILE. May just want to print summary for piping.)
+ *
+ * Cell flags:
+ * count : number of cells to generate
+ * diversity factor : factor by which CDR3s are more diverse than CDR1s
+ * output : name of the output file
+ *
+ * Plate flags:
+ * cellfile : name of the cell sample file to use as input
+ * wells : the number of wells on the plate
+ * dist : the statistical distribution to use
+ *      (if exponential) lambda : the lambda value of the exponential distribution
+ *      (if gaussian) stddev : the standard deviation of the gaussian distribution
+ * rand : randomize well populations, take a minimum argument and a maximum argument
+ * populations : number of t cells per well per section (number of arguments determines number of sections)
+ * dropout : plate dropout rate, double from 0.0 to 1.0
+ * output : name of the output file
+ *
+ * Graph flags:
+ * cellfile : name of the cell sample file to use as input
+ * platefile : name of the sample plate file to use as input
+ * output : name of the output file
+ *
+ * Match flags:
+ * graphFile : name of graph and data file to use as input
+ * min : minimum number of overlap wells to attempt a matching
+ * max : the maximum number of overlap wells to attempt a matching
+ * maxdiff : (optional) the maximum difference in occupancy to attempt a matching
+ * minpercent : (optional) the minimum percent overlap to attempt a matching.
+ * writefile : (optional) the filename to write results to
+ * output : the values to print to System.out for piping
+ *
+ */
 public class CommandLineInterface {
 
     public static void startCLI(String[] args) {
@@ -20,7 +59,7 @@ public class CommandLineInterface {
                 .longOpt("make-plates")
                 .desc("Makes a sample plate file")
                 .build();
-        Option makeGraph = Option.builder("graoh")
+        Option makeGraph = Option.builder("graph")
                 .longOpt("make-graph")
                 .desc("Makes a graph and data file")
                 .build();