Gwas report with non human genome

[LouisLeNezet]

Hi,

Thanks a lot for your wonderful tool !

I'm trying to run the nf-gwas pipeline that use your genomic-utils tools.
I'm working with dogs, and I had some trouble making it work.

I've nearly succeed, but now the

java -jar /opt/genomic-utils.jar gwas-report

Crash due to non recognise chromosome name, I think.

java.lang.NullPointerException: Cannot invoke "java.lang.Integer.intValue()" because the return value of "java.util.Map.get(Object)" is null
	at genepi.genomic.utils.commands.gwas.binner.Chromosome.getOrder(Chromosome.java:27)
	at genepi.genomic.utils.commands.gwas.report.manhattan.ManhattanPlot.getBin(ManhattanPlot.java:80)
	at genepi.genomic.utils.commands.gwas.report.manhattan.ManhattanPlot.setPeaks(ManhattanPlot.java:103)
	at genepi.genomic.utils.commands.gwas.GwasReportCommand.createHtmlReport(GwasReportCommand.java:354)
	at genepi.genomic.utils.commands.gwas.GwasReportCommand.call(GwasReportCommand.java:220)
	at genepi.genomic.utils.commands.gwas.GwasReportCommand.call(GwasReportCommand.java:30)
	at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
	at picocli.CommandLine.access$1500(CommandLine.java:148)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
	at picocli.CommandLine.execute(CommandLine.java:2170)
	at genepi.genomic.utils.App.main(App.java:68)

Would it be possible to add a parameter in the gwas-report command to set the max number of chromosome ?

If I'm not wrong the aim would be to change the Chromosome class in the binner to set a max value instead of 22 in

static {
		for (int i = 1; i <= 22 + 1; i++) {
			CHROM_ORDERS.put(i + "", i);
		}
		CHROM_ORDERS.put("X", CHROM_ORDERS.size());
		CHROM_ORDERS.put("Y", CHROM_ORDERS.size());
		CHROM_ORDERS.put("MT", CHROM_ORDERS.size());
	}

Thanks a lot for your help !