update readme and add Zipf exponent option to CLI

readme.md

@@ -136,7 +136,7 @@ There are a number of command line options, to allow the program to be used in s
 `java -jar BiGpairSEQ_Sim.jar -help`
 
 ```
-usage: BiGpairSEQ_Sim.jar
+ usage: BiGpairSEQ_Sim.jar
  -cells,--make-cells   Makes a cell sample file of distinct T cells
  -graph,--make-graph   Makes a graph/data file. Requires a cell sample
                        file and a sample plate file
@@ -156,6 +156,8 @@ usage: BiGpairSEQ_Sim.jar -plate
  -c,--cell-file <filename>     The cell sample file to use
  -d,--dropout-rate <rate>      The sequence dropout rate due to
                                amplification error. (0.0 - 1.0)
+ -exp <value>                  If using -zipf flag, exponent value for
+                               distribution
  -exponential                  Use an exponential distribution for cell
                                sample
  -gaussian                     Use a Gaussian distribution for cell sample
@@ -173,6 +175,7 @@ usage: BiGpairSEQ_Sim.jar -plate
  -stddev <value>               If using -gaussian flag, standard deviation
                                for distrbution
  -w,--wells <number>           The number of wells on the sample plate
+ -zipf                         Use a Zipf distribution for cell sample
 
 usage: BiGpairSEQ_Sim.jar -graph
  -c,--cell-file <filename>                Cell sample file to use for
@@ -234,7 +237,6 @@ usage: BiGpairSEQ_Sim.jar -match
                                to stdout.
  -pv,--p-value                 (Optional) Calculate p-values for sequence
                                pairs.
-
 ```
 
 ### INTERACTIVE INTERFACE