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statgen / bamUtil

http://genome.sph.umich.edu/wiki/BamUtil
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Add explicit usage commands #25

Closed jonathonl closed 8 years ago

jonathonl commented 8 years ago

This expands on previous merge from rleonid. It includes help/usage commands for individual tools and outputs usage to stdout. Some minor bugs only affecting OS X are also included.

pjvandehaar commented 8 years ago

Do you understand why https://travis-ci.org/statgen/bamUtil/builds/121457794#L770 and https://travis-ci.org/statgen/bamUtil/builds/121460405#L770 failed? I have no idea. If you don't know, maybe that long && chain should do more printing.

Maybe talk to Hyun or Mary Kate about how you should deal with putting commits into master. If it were me, I'd probably just merge it. These changes all make sense, and the tests are passing with a reasonably old version of gcc.

I don't know how to go about releasing a new version. Let's talk about that sometime, unless you've already figured it out.

jonathonl commented 8 years ago

Yeah, I fixed those failures in the subsequent push. The output from each shell script is suppressed when running from make, but visible when running the scripts individually.

I made a PR for the sake of documenting the merge. Since I'm probably going to be the one merging all of these, it's probably going to make more sense to just merge locally and push to master in the future.

Mary Kate did mention versioning master was kind of up in the air at this point. So yes, let's talk about this.