Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Browse files
Browse the repository at this point in the history
Create README.TXT
- Loading branch information
Showing
1 changed file
with
39 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,39 @@ | ||
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 |