igvtools count --minMapQuality command line option broken

[sg550]

Hi IGV Team,

There seems to be a command line parsing error in igvtools when using --minMapQuality option.

Program: igvtools. IGV Version 2.1.7 (2413)04/27/2012 11:47 PM

$ ~/src/IGVTools/igvtools count -z 5 -w 25 -e 250 --minMapQuality 1 test.bam test.tdf hg19
Exception in thread "main" java.lang.ClassCastException: java.lang.String cannot be cast to java.lang.Integer
at org.broad.igv.tools.IgvTools.run(IgvTools.java:297)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:192)

Best regards,
Stefan

[jsilter]

Thanks for letting us know. Will be fixed in the next release

[sg550]

I have just downloaded and tested version 2.1.24 and it doesn't seem to be
fixed yet. I still get:

$ ~/src/IGVTools/igvtools count -z 5 -w 1000 -e 250 --minMapQuality 37
reads/Project_ALANGLEY/bam/Sample_ARL01_HiSeq.regions_excluded.bam
Sample_ARL01_HiSeq.regions_excluded.bam.wig hg19
Exception in thread "main" java.lang.ClassCastException: java.lang.String
cannot be cast to java.lang.Integer
at org.broad.igv.tools.IgvTools.run(IgvTools.java:297)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:192)

BW,
Stefan

On 4 September 2012 16:03, Jacob Silterra notifications@github.com wrote:

Thanks for letting us know. Will be fixed in the next release

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-8266150.

[jsilter]

Point releases don't contain all bugfixes. The fix is in the github source tree, and in the EA build of igvtools at http://www.broadinstitute.org/software/igv/download_dev.