Getting Help

hgvs always works and has no bugs. Furthermore, its interface is so easy to use that a manual is unnecessary.

Just kidding.

While hgvs is well-tested and has been used by many groups for several years, bugs, unexpected behaviors, and other questions occur. Fortunately, there’s a small community of people who can help.

If you need help, please read the following sources first. Then, if you’ve still got a question, post to one of them.

If you have questions about the Variation Nomenclature Recommendations, consider posting your questions to the HGVS Facebook page.

hgvs-discuss Mailing List/Group

For general questions, the best source of information is the hgvs-discuss Google Group (https://groups.google.com/forum/#!forum/hgvs-discuss). It is publicly visible, but posting requires joining in order to control spam. The mailing list is the preferred way to reach the hgvs package authors. (Please do NOT send email directly to authors.)

Slack Workspace

See the [biocommons community page](https://github.com/biocommons/biocommons) for information about how to join.

Bug Reports

If you think you’ve got a bug, please report it! Here are a few tips to make it more likely that you get a useful reply:

  • Use the command-line tool hgvs-shell that comes with hgvs to prepare your bug report. Using hgvs-shell makes it easier for you to report the bug and make it easier for developers to understand it.
  • Take the time to prepare a minimal example that demonstrates the bug. You are unlikely to get a reply if you submit a report that includes your own wrappers and tooling.
  • Include the bug demonstration as text. A screenshot of a bug report is not reproducible.
  • Include the values of hgvs.__version__ and hgvs.hdp.url, and whether you’re using seqrepo. (i.e., whether you specified HGVS_SEQREPO_DIR)
  • hgvs-shell in an upcoming release will provide much of the above information for you, as shown below. Please use it.
  • Include an explanation of the result you expected and why.
  • Report the bug using github, which requires an account. If you don’t have an account (and don’t want to create one), sending the same information to the mailing list is acceptable.
$ hgvs-shell

############################################################################
hgvs-shell -- interactive hgvs
hgvs version: 1.1.3.dev11+ne7b6a1c3ec7a
data provider url: postgresql://anonymous:anonymous@uta.biocommons.org/uta/uta_20170117
schema_version: 1.1
data_version: uta_20170117
sequences source: remote (bioutils.seqfetcher)

The following variables are defined:
* hp -- hgvs parser
* hdp -- hgvs data provider
* vm -- VariantMapper
* am37 -- AssemblyMapper, GRCh37
* am38 -- AssemblyMapper, GRCh38
* hv -- hgvs Validator
* hn -- hgvs Normalizer

hgvs_g, hgvs_c, hgvs_p -- sample variants as hgvs strings
var_g, var_c, var_p -- sample variants, as parsed SequenceVariants

When submitting bug reports, include the version header shown above
and use these variables/variable names whenever possible.

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