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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 | ||
| 5 |