Update Readme

readme.md

@@ -105,6 +105,7 @@ The program's caching behavior can be controlled in the Options menu. By default
 The program can optionally output Graph/Data files in .GraphML format (.graphml) for data portability. This can be 
 turned on in the Options menu. By default, GraphML output is OFF.
 
+---
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
 four sequences: Alpha CDR3, Beta CDR3, Alpha CDR1, Beta CDR1. The sequences are represented by
@@ -122,7 +123,6 @@ Comments are preceded by `#`
 
 Structure:
 
----
     # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
 | Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
 |---|---|---|---|
@@ -167,7 +167,6 @@ Dropout sequences are replaced with the value `-1`. Comments are preceded by `#`
 
 Structure:
 
----
 ```
 # Cell source file name:
 # Each row represents one well on the plate
@@ -223,7 +222,6 @@ Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
 
 Example output:
 
----
 ```
 # Source Sample Plate file: 4MilCellsPlate.csv
 # Source Graph and Data file: 4MilCellsPlateGraph.ser
@@ -290,7 +288,7 @@ slightly less time than the simulation itself. Real elapsed time from start to f
   * ~~Apache Commons CSV library writes entries a row at a time~~ 
     * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
 * ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
-  * ~~Custom vertex type with attribute for sequence occupancy?~~ABANDONED
+  * ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED
     * Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.
 * Re-implement command line arguments, to enable scripting and statistical simulation studies
 * Re-implement CDR1 matching method