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LiuLabUB / HMMRATAC

HMMRATAC peak caller for ATAC-seq data
GNU General Public License v3.0
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Q: Error when using bedgraph option： Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException #91

Open jamesc99 opened 2 years ago

jamesc99 commented 2 years ago

Hey, I am using hmmr and I encountered some problems. when I use the default syntax (java -jar HMMRATAC_V1.2.4_exe.jar -b ATACseq.sorted.bam -i ATACseq.sorted.bam.bai -g genome.info), it works good. but when I add a --bedgraph option to it (java -jar HMMRATAC_V1.2.4_exe.jar -b ATACseq.sorted.bam -i ATACseq.sorted.bam.bai -g genome.info --bedgraph), I will get error below:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 7 at HMMR_ATAC.ArgParser.set(ArgParser.java:383) at HMMR_ATAC.ArgParser.(ArgParser.java:70) at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:104)

I dont know why and I would be really appreciate if you have any idea. thanks

EvanTarbell commented 2 years ago

You have to put the word "True" after --bedgraph. ie: java -jar HMMRATAC_V1.2.4_exe.jar -b ATACseq.sorted.bam -i ATACseq.sorted.bam.bai -g genome.info --bedgraph True --bedgraph isnt a "flag" option, so the argument parser (which is throwing the error) is expecting something after it. Hope this helps