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 usages questions occur. Fortunately, there’s now 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.

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.

Please do NOT send email directly to authors.

Gitter Channel

We have a new gitter community at https://gitter.im/biocommons/hgvs. There’s not much use yet, but there’s a chance that you could get real-time replies there.

Bug Reports

If you think you’ve got a bug, please report it using github (requires a github account). 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.
$ 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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