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broadinstitute / rigerj

Java implementation of RIGER and other gene enrichment methods, useful for RNAi and CRISPR screen analysis.
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Issue list table exceeds 100,000 #20

Open BioInfrookie opened 1 hour ago

BioInfrookie commented 1 hour ago

Hello, I've encountered a problem where the number of rows in my list table exceeds 100,000. How can I resolve this issue? Thank you for your assistance.

$java -jar /home/qzh/software/rigerj/target/rigerj-2.0.3-assembly.jar -scoringMethod SecondBestRank -inputFile Merge_sgRNA_fold_rank.txt -outputFile tmp Exception in thread "main" java.lang.NumberFormatException: For input string: "1e+05" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.<init>(Integer.java:867) at org.broadinstitute.gpp.rigerj.RigerJMain.createHairpinDatas(RigerJMain.java:202) at org.broadinstitute.gpp.rigerj.RigerJMain.buildRigerInputs(RigerJMain.java:156) at org.broadinstitute.gpp.rigerj.RigerJMain.runRigerJ(RigerJMain.java:143) at org.broadinstitute.gpp.rigerj.RigerJMain.main(RigerJMain.java:57)

BioInfrookie commented 1 hour ago

$ cat Merge_sgRNA_fold_rank.txt | wc -l 100001

tmgreen commented 11 minutes ago

Thanks for bringing this to our attention. I've put in a pull request to fix it: https://github.com/broadinstitute/rigerj/pull/21