Closed yuanyuan12543 closed 6 months ago
ofiryaish
commented
6 months ago Hi,
I think this is because you did not insert the Best in-a-window size argument. The README was wrong by saying to insert only if Best in-a-window is true. I fixed it now.
Please confirm or tell me if this is not the problem.
Thank you for pointing this out!
ofiryaish
commented
6 months ago @yuanyuan12543 Can you please confirm the issue is solved?
yuanyuan12543
commented
6 months ago Sorry for forgetting to do so. Yes. The issue is solved.
Thank you ！
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@yuanyuan12543 https://github.com/yuanyuan12543 Can you please confirm the issue is solved?
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Hi, I am trying to run the code below, java -cp bin SmithWatermanOffTarget.SmithWatermanOffTargetSearchAlign /blue/vulpe/zjl1983/var/chromosome/canFam6/canFam6.fa sgRNA_titin.txt SWOF 4 5 5 2 1 false NGG false
However, I got the error message as below, Exception in thread "main" java.lang.NumberFormatException: For input string: "NGG" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:665) at java.base/java.lang.Integer.parseInt(Integer.java:781) at SmithWatermanOffTarget.SmithWatermanOffTargetSearchAlign.main(SmithWatermanOffTargetSearchAlign.java:630)
This is my sgRNA.txt file ATTGCCGCAGGTTCTGGAACNGG CCTCAGTACAAGTTTCAGGTNGG AGTACAAGTTTCAGGTTGGTNGG CAAGTTTCAGGTTGGTTGGTNGG
I could not figure out the reason for the error, could you please help me out?
Thank you!