Program group reorganization

[cmnbroad]

Reorganize program group categories and tool assignments, per @vdauwera. There are 3 separate commits; one with the new program group class definitions; one with the tool assignments; and one to delete the obsolete program groups.

Checklist (never delete this)

• Added or modified tests to cover changes and any new functionality
• Edited the README / documentation (if applicable)
• All tests passing on Travis

Review

• Final thumbs-up from reviewer
• Rebase, squash and reword as applicable

[coveralls]

Coverage decreased (-0.03%) to 77.621% when pulling c15fa46 on cn_program_groups into 7c0980b on master.

[sooheelee]

Everything looks great with one exception.

MakeSitesOnlyVcf should be under Variant Manipulation. Currently, it is under Variant Evaluation and Refinement.

Thank you for all this work.

[sooheelee]

programGroup = VariantManipulationProgramGroup.class

[sooheelee]

I am good with these. @vdauwera Will you want to review too?

[coveralls]

Coverage decreased (-0.03%) to 77.621% when pulling 9928091 on cn_program_groups into a86b2fc on master.

[coveralls]

Coverage decreased (-0.03%) to 77.621% when pulling 9928091 on cn_program_groups into a86b2fc on master.

[vdauwera]

Ah, I had already looked at it but failed to post my review. All looks good to me!

[sooheelee]

👍🏽

[ktibbett]

I followed the directions for checking out and testing this PR. When I try to run it in the old picard-style without arguments (which should give a list of the tools and their program groups) I get the following error:

Exception in thread "main" java.lang.RuntimeException: The following classes are missing the required CommandLineProgramProperties annotation: CollectWgsMetricsFromQuerySorted, DummyProgram
at picard.cmdline.PicardCommandLine.extractCommandLineProgram(PicardCommandLine.java:132)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:93)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

[cmnbroad]

@ktibbett Hi Kathleen - I'm not sure what directions you're referring to, but CollectWgsMetricsFromQuerySorted has been removed from the Picard repo for a while now (I have no idea what DummyProgram is). Are you sure you did a clean build from this branch ? If I pull this PR and build it, and just run the jar, I get the tool/program group list as expected.

[vdauwera]

@ktibbett all basic invocations work for me -- @ktibbett, can you post the command you ran?

[vdauwera]

@nh13 @tfenne Would you care to review this? This PR affects how tool docs are categorized; the main driver was to standardize doc categories across Picard and GATK ahead of the GATK 4.0 release, which will produce more user-friendly documentation fro both projects. Shouldn't affect anything on the dev side, except if you have any open branches you'll need to rebase to take in the new program group definitions.

We're hoping to get this merged ASAP once everything checks out in order to finalize preparations on the GATK side, so we would need a quick turnaround. Thanks!

[sooheelee]

@ktibbett, I don't know what old picard-style without arguments refers to. Can you please clarify?

I think the following will be helpful to you.

I built a jar off of this branch and if I run java -jar build/libs/picard.jar -h, I see an index of tools that reflect the new categorization, e.g.:

I am able to look at tool-specific documentation, e.g. with java -jar build/libs/picard.jar FifoBuffer --help:

Sidenote for @cmnbroad: If I run --list instead of -h I get the same tool list and a funny message at the end:

'--list' is not a valid command. See PicardCommandLine -h for more information.

[ktibbett]

@vdauwera / @sooheelee , I did a clean checkout and this time it worked; apologies.

[sooheelee]

We've waited till EOD for input from @nh13 @tfenne and so will proceed assuming this is all agreeable with them. Since this PR is a blocker for many other Picard program group assignments, I will go ahead and merge. look into why there are conficts when before there were none.

[sooheelee]

Looks like these are due to other doc update PRs that have since been merged. Sorry about that @cmnbroad. Hope you find them easy to resolve.

[nh13]

Sorry but I am on vacation so I won’t be able to review. The amount of documentation changes is a bit overwhelming to follow, especially over the holidays! The changes also differ significantly from how I write documentation (not a bad thing, just different), so I will pass on reviewing any documentation changes and focus on functional changes moving forward. Thanks for pushing on all these PRs and including me.

[coveralls]

Coverage decreased (-0.03%) to 77.654% when pulling 5fab7db on cn_program_groups into d8b7653 on master.