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.
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.
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.
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. In [1]: