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polysomy command is not in help output when USE_GPL=1 #280

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tseemann opened this issue Jun 12, 2015 · 0 comments
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polysomy command is not in help output when USE_GPL=1 #280

tseemann opened this issue Jun 12, 2015 · 0 comments

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@tseemann
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I compiled bcftools with USE_GPL=1 to enable the polysomal command.

However it does not appear in the --help output like the other commands.

I think it is because the .help field has a `-`` (dash) at the start which seems to be a code to "not advertise" this option:

#if USE_GPL
    { .func  = main_polysomy,
      .alias = "polysomy",
      .help  = "-detect number of chromosomal copies",
    },
#endif
    { .func  = main_vcfsom,
      .alias = "som",
      .help  = "-filter using Self-Organized Maps (experimental)"   // do not advertise
  },

I'm guessing this is a legacy bug due to the licence issues around GSL, but if we explicity asked for it then it should be in the help.
mcshane added a commit that referenced this issue Jul 6, 2015
@mcshane
show polysomy command in help message
9480a54 
This was hidden as it was/is experimental, but with the licensing
additions, users are explicitly requesting the command by compiling
with USE_GPL=1, so we might as well display in the help message.

Closes #280
@mcshane mcshane mentioned this issue Jul 6, 2015
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pd3 pushed a commit to pd3/bcftools that referenced this issue Jul 12, 2015
@mcshane @pd3
show polysomy command in help message
b508d0e 
This was hidden as it was/is experimental, but with the licensing
additions, users are explicitly requesting the command by compiling
with USE_GPL=1, so we might as well display in the help message.

Closes samtools#280
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@tseemann