updated to allow custom medMAD file input

README

@@ -43,7 +43,7 @@ To build and run GRASPER, the following are required:
 
 - a reference genome sequence
 
-- .medMAD file containing meadian and Median Absolute Deviation (MAD) values for library insert size. 1 SD ~ 1.4826 MAD (https://en.wikipedia.org/wiki/Median_absolute_deviation) under normal distribution. This file contains single line of 2 values delimited by a tab.
+- as of v0.1.1, .medMAD file is generated AUTOMATICALLY from RepGraph (v 0.1.1). This file contains meadian and Median Absolute Deviation (MAD) values for library insert size. 1 SD ~ 1.4826 MAD (https://en.wikipedia.org/wiki/Median_absolute_deviation) under normal distribution. This file contains single line of 2 values delimited by a tab.
 
 -------------------------
       Installation

src/Constants.java

@@ -264,11 +264,11 @@ public static void loadConstants(String configFile, boolean suppressmsg, boolean
 	    }
 	    br.close();
 	    if(loadMedMAD){
-		if(Constants.MEDMADFILE.equals("")){
+		if(Constants.MEDMADFILE.equals(""))
 		    Constants.MEDMADFILE = Constants.PROJNAME + ".medMAD_GRASPER";
-		    Constants.loadMedMAD(Constants.MEDMADFILE);
-		    Constants.updateConstants();
-		}
+				
+		Constants.loadMedMAD(Constants.MEDMADFILE);
+		Constants.updateConstants();
 	    }else{
 		Constants.updateConstants();
 	    }

test_data/example_config.txt

@@ -1,5 +1,5 @@
 #PATH to RepGraph package is installed.
-REPGRAPH_BIN=/u/heewlee/ABruijn/blast2rep_blastFIX/
+REPGRAPH_BIN=/home/data1/groups/heewlee/MA/Simulation_data/eColi_ABruijn/NEW6_TANDEM/IU_GIT/RepGraph
 
 #PATH to the bin directory under GRASPER installation directory
 GRASPER_BIN=/data/groups/heewlee/MA/Simulation_data/eColi_ABruijn/NEW6_TANDEM/IU_GIT/GRASPER/bin