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Cleaning up formatting and spacing of docs. #1640

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merged 4 commits into from Aug 3, 2017

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devin-petersohn commented Jul 26, 2017

Resolves #1638.

Wrapped lines at 80 if possible, also addressed formatting and spacing issues from rendering of the doc.

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Coverage Status

Coverage remained the same at 83.961% when pulling 76913b9 on devin-petersohn:issue#1638 into c8a2202 on bigdatagenomics:master.

coveralls commented Jul 26, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 76913b9 on devin-petersohn:issue#1638 into c8a2202 on bigdatagenomics:master.

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Test PASSed.
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@fnothaft

Few small nits. Thanks @devin-petersohn!

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@@ -77,7 +83,7 @@ Add the new command to the default list of commands in `ADAMMain`.
Build ADAM and run the new command via `adam-submit`.
```bash
```

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fnothaft Jul 26, 2017

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Please revert deletion of bash.

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fnothaft Jul 26, 2017

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Please revert deletion of bash.

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devin-petersohn Jul 26, 2017

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I deleted the bash specification here because it caused non-bash text to render with text highlighting. Removing bash does not affect anything except the incorrectly highlighted text. In the rendered version of this PR, you can see an example of both bash tagged and not.

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devin-petersohn Jul 26, 2017

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I deleted the bash specification here because it caused non-bash text to render with text highlighting. Removing bash does not affect anything except the incorrectly highlighted text. In the rendered version of this PR, you can see an example of both bash tagged and not.

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fnothaft Jul 26, 2017

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Ah, I see. Thanks for the clarification; I thought it was an incidental deletion, but you are right, this should not be bash formatted.

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fnothaft Jul 26, 2017

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Ah, I see. Thanks for the clarification; I thought it was an incidental deletion, but you are right, this should not be bash formatted.

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Coverage Status

Coverage remained the same at 83.961% when pulling 1bf855b on devin-petersohn:issue#1638 into c8a2202 on bigdatagenomics:master.

coveralls commented Jul 31, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 1bf855b on devin-petersohn:issue#1638 into c8a2202 on bigdatagenomics:master.

@fnothaft

Couple of small last fixes we should get in. Thanks @devin-petersohn!

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Extend `Args4jBase` class to specify arguments to the command. Arguments are defined using
the [args4j library](http://args4j.kohsuke.org/). If reading from or writing to Parquet,
consider including Parquet arguments via `with ParquetArgs`.
1. [Extend Args4jBase to specify arguments](#extend-arguments)

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devin-petersohn Aug 3, 2017

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How does this look @fnothaft?

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devin-petersohn Aug 3, 2017

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How does this look @fnothaft?

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fnothaft Aug 3, 2017

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I think this looks great, thanks @devin-petersohn!

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fnothaft Aug 3, 2017

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I think this looks great, thanks @devin-petersohn!

* Use ADAM as a [library in new applications](#library)
## Extend the ADAM CLI by adding new commands {#commands}
ADAM's CLI is implemented in the adam-cli Apache Maven module of the
[bdgenomics/adam](https://github.com/bigdatagenomics/adam) repository, one
.scala source file for each CLI action (e.g. [Transform.scala](https://github.com/bigdatagenomics/adam/blob/master/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala)
for the [transform](#transform) action), and a main class ([ADAMMain.scala](https://github.com/bigdatagenomics/adam/blob/master/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala))
.scala source file for each CLI action (e.g.

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devin-petersohn Aug 3, 2017

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I thought about rephrasing this a little bit because the flow gets broken by each example. Thoughts?

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devin-petersohn Aug 3, 2017

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I thought about rephrasing this a little bit because the flow gets broken by each example. Thoughts?

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fnothaft Aug 3, 2017

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I think this is fine as is, but if you'd like to make a pass at touching it up, that's a-OK with me.

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fnothaft Aug 3, 2017

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I think this is fine as is, but if you'd like to make a pass at touching it up, that's a-OK with me.

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devin-petersohn Aug 3, 2017

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Let's go with the "if it's not broken, don't fix it" principle here. We can leave as-is.

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devin-petersohn Aug 3, 2017

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Let's go with the "if it's not broken, don't fix it" principle here. We can leave as-is.

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fnothaft Aug 3, 2017

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SGTM!

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fnothaft Aug 3, 2017

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SGTM!

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devin-petersohn Aug 3, 2017

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Thanks for your patience. I have a couple of comments I'd like feedback on.

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devin-petersohn commented Aug 3, 2017

Thanks for your patience. I have a couple of comments I'd like feedback on.

@fnothaft fnothaft merged commit 96fc37f into bigdatagenomics:master Aug 3, 2017

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codacy/pr Good work! A positive pull request.
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Merged! Thanks @devin-petersohn!

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fnothaft commented Aug 3, 2017

Merged! Thanks @devin-petersohn!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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