Q: Error when using bedgraph option： Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException

[jamesc99]

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]

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