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Create README.TXT

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sus11005 committed Sep 28, 2016
1 parent d1c36be commit 10495a3d1a788576dfc2af1fa2922b2c632fef25
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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

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