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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. | ||
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Please follow the instruction below: | ||
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(1) Compile the classes: | ||
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>javac Contig.java | ||
>javac Position.java | ||
>javac Utilities.java | ||
>javac Assembly.java | ||
>javac Utils.java | ||
>javac Driver.java | ||
>chmod 777 * | ||
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(2) Run the tool: | ||
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>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 | ||
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(3) 7zip executable files should be in the running directory. | ||
For convenience we have already provided the executables. | ||
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(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. | ||
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(5) properties.prop contains: | ||
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#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 | ||
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