ivgtools count --query command line format question

[jspai...@otogenetics.com]

How do I use --query in the count command line?

I am using:

java -Xmx1000m  -Djava.awt.headless=true -jar igvtools.jar count --query IVGInhCa.bed -w 1 my.bam my.wig hg19.genome

where IVGInhCa.bed is formatted as:

chr2:215593389-215593742

chr2:215595124-215595242

chr2:215609780-215609893

chr2:215610435-215610588

chr2:215617160-215617289

chr2:215632195-215632388

chr2:215633945-215634046

+600 more regions

I get the error:

Error parsing queryString

In the online manual it says:

--query [querystring]

     Only count a specific region. Query string has syntax <chr>:<start>-<end>. e.g. chr1:100-1000. Input file must be indexed. 

I am afraid I do not understand this.

Could someone help me figure out where my formatting erorr is in my .bed file?

Thank you

-John Spainhour

[jspai...@otogenetics.com]

I am getting an error after hg19 is loaded:

ERROR [2018-07-18 09:23:51,579]  [IgvTools.java:891] [main]  Error parsing queryString: IVGInhCa.bed

java.lang.IllegalArgumentException: Error parsing queryString: IVGInhCa.bed

        at org.broad.igv.tools.CoverageCounter.parseOptions(CoverageCounter.java:227)

        at org.broad.igv.tools.CoverageCounter.<init>(CoverageCounter.java:198)

        at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:873)

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:376)

        at org.broad.igv.tools.IgvTools.main(IgvTools.java:259)

Error parsing queryString: IVGInhCa.bed

java.lang.IllegalArgumentException: Error parsing queryString: IVGInhCa.bed

        at org.broad.igv.tools.CoverageCounter.parseOptions(CoverageCounter.java:227)

        at org.broad.igv.tools.CoverageCounter.<init>(CoverageCounter.java:198)

        at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:873)

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:376)

        at org.broad.igv.tools.IgvTools.main(IgvTools.java:259)

Done