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[ADAM-1342] Update CLI docs after #1288 merged. #1343

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@fnothaft
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fnothaft commented Jan 6, 2017

Resolves #1342. Adds validation stringency documentation for vcf2adam and adam2vcf. Removes mention of the anno2adam and flatten commands, which were removed in #1288.

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AmplabJenkins commented Jan 6, 2017

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@@ -330,6 +311,19 @@ options](#default-args). Additionally, `adam2vcf` takes the following options:
* `-single`: Saves the VCF file as headerless shards, and then merges the
sharded files into a single VCF.

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heuermh Jan 6, 2017

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Needs a line like

  • -stringency: Sets the validation stringency for various checks. Defaults to STRICT. See validation stringency for more details.
@heuermh heuermh added this to the 0.21.0 milestone Jan 6, 2017
Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.
@fnothaft fnothaft force-pushed the fnothaft:issues/1342-vcf-adam-cli-doc-update branch from ae9d54c to 0873de1 Jan 6, 2017
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fnothaft commented Jan 6, 2017

Rebased and addressed comment.

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AmplabJenkins commented Jan 6, 2017

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1724/
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heuermh approved these changes Jan 6, 2017
@heuermh heuermh merged commit f3c064c into bigdatagenomics:master Jan 6, 2017
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heuermh commented Jan 6, 2017

Thank you, @fnothaft

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