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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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LiLaC error: Unrecognized option: -gene_copy_number_file #316

Closed Biojenifer closed 2 years ago

Biojenifer commented 2 years ago

Hi!

Do you know which is the new name of this argument for lilac_v1.3_rc2.jar: -gene_copy_number_file?

I get the following error:

Exception in thread "main" org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -gene_copy_number_file at org.apache.commons.cli.DefaultParser.handleUnknownToken(DefaultParser.java:347) at org.apache.commons.cli.DefaultParser.handleConcatenatedOptions(DefaultParser.java:689) at org.apache.commons.cli.DefaultParser.handleShortAndLongOption(DefaultParser.java:520) 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.lilac.LilacApplication.createCommandLine(LilacApplication.java:763) at com.hartwig.hmftools.lilac.LilacApplication.main(LilacApplication.java:737)

I am using this version because I'm trying to resolve the same error explained in this post

Thanks!

charlesshale commented 2 years ago

I've just updated the READ-ME - the config name is 'gene_copy_number'.