Incorrect HGVS name creation from VCF file about myvariant.info HOT 4 CLOSED

Whenever using the function get_hgvs_from_vcf, variants with two entries as Alt allele (for instance https://samtools.github.io/hts-specs/VCFv4.2.pdf, 3rd and 5th variant on the vcf sample file) gain its own place in the list of variants extracted from the VCF file. This was noticed when running mv.getvariants(variant_list) and getting as output a few more variants than originally expected.

As a preview of what myvariant outputs in those instances:
{u'query': u'GTTT', u'notfound': True}
{u'query': u'CAAAAAAAAA', u'notfound': True}
{u'query': u'AGTGT', u'notfound': True}
...
{u'query': u'AGTTTT', u'notfound': True}

from myvariant.info.

Hi Mazzafish,

This should be an issue for myvariant.py repo. We have just solved this issue where an ALT column has multiple alleles. We also made some improvement on the handling of some other VCF edge cases.

from myvariant.info.

Awesome, I'll test it out. Thanks for the response.

from myvariant.info.

And just a note, you will need to test the latest code from myvariant.py repo, as we have not released a new version to PyPI yet.

from myvariant.info.