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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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How to pull out all the option for GRIPSS? #286

Closed zhujack closed 2 years ago

zhujack commented 2 years ago

Hi,

I try to pull out all the options for GRIPSS from the command line? I always get the following error:

   `$ java -jar /data//hmftools/gripss_2.1.jar -h

    Exception in thread "main" org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -h
at org.apache.commons.cli.DefaultParser.handleUnknownToken(DefaultParser.java:347)
at org.apache.commons.cli.DefaultParser.handleShortAndLongOption(DefaultParser.java:484)
at org.apache.commons.cli.DefaultParser.handleToken(DefaultParser.java:243)
at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:120)
at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:76)
at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:60)
at com.hartwig.hmftools.gripss.GripssApplication.createCommandLine(GripssApplication.java:345)
at com.hartwig.hmftools.gripss.GripssApplication.main(GripssApplication.java:331)`

Also it looks like minNormalCoverage option does not exist for GRIPSS:

    `java -jar /data/source/hmftools/gripss_2.1.jar -minNormalCoverage 5 ...

     Exception in thread "main" org.apache.commons.cli.UnrecognizedOptionException: 
     Unrecognized option: -minNormalCoverage`

Any suggestions will be greatly appreciated.

Jack

charlesshale commented 2 years ago

I will add '-h' support for the next version.

I have added the missing config options to the READ-ME. MinNormalCoverage can be set with 'min_normal_coverage'.