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yinxc / structural-information-minimisation

Code of structural entropy minimisation for TAD identification of Hic matrix
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How to run this software? #2

Open zhixuqiu opened 6 years ago

zhixuqiu commented 6 years ago

I want to use your software deDoc. Although the Hi-C matrix was same as the description of readme text for deDoC, there are some strange error when I used it. Could you help me about this? I would appreciate is if you can give me a hand!

The error like this: /home/qiuzx/software/packages_save/deDoc$ java -jar deDoc.jar hictest.matrix deDoc(E) begin: 2018-09-02 20:41:04 Exception in thread "main" java.lang.NumberFormatException: For input string: "1 1 536.0" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at filerw.Tool.GetGraph(Tool.java:27) at main.deDoc.dedoc(deDoc.java:26) at main.deDoc.main(deDoc.java:17)

matthewpendleton commented 6 years ago

You need to have the first line contain the number of entries in the file.

matthewpendleton commented 6 years ago

so the head of your file should look like this:

239485724933 1 1 536.0 1 2 18465.0 2 1 18465.0

for a file that contains 239485724933 total entries (which should be equal to the square of the number of bins in the genome at the given resolution minus the number of bins containing zero read support).

yinxc commented 5 years ago

the first line is the number of bins in the hic matrix

When-Turing-met-Darwin commented 3 months ago

based on my testing，the first line should be the size(or more than it?) of hic matirx such as the matrix: 1 3 1.0 1 50 3.0 200 3 1.1

the first line may be 200