Create README.TXT

COMPRESSION/README.TXT

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+Please, compile and run the code in Linux machine.
+Java source code is compiled and run by Java Virtual Machine (JVM) 1.6.0.
+
+Please follow the instruction below:
+
+(1) Compile the classes:
+
+    >javac Contig.java
+    >javac Position.java
+    >javac Utilities.java
+    >javac Assembly.java
+    >javac Utils.java
+    >javac Driver.java
+	>chmod 777 *
+
+(2) Run the tool:
+
+    >java Driver <reference_file_name> <target_file_name> <compressed_file_name>	
+    This command will produce <compressed_file_name>.7z archive file
+	Example: java Driver chr_ko224_21.fa chr_hg18_21.fa chr21.nrgc
+	The above command will produce chr21.nrgc.7z
+
+(3) 7zip executable files should be in the running directory.
+    For convenience we have already provided the executables.
+
+(4) properties.prop file is an interface. Users can change some variables according to their needs. 
+    We have used default values. If the tool exits outputing "System is exiting..." users should 
+	increase the "division length" to get compress the file.
+
+(5) properties.prop contains:
+
+    #division length - segments containing the bases
+    500000
+    #pattern - fingerprint/barcode
+    ACTAC
+    #compute pattern - if "on" the tool will generate the fingerprint
+    off
+    #pattern length - length of the fingerprint
+    5