Dave Lawrence

Crash reading valid but weird VCF

7

Hi, I'm getting strange genotype calls and then a crash with my GATK VCF. The zygosity call is strange, but the VCF passes validation. I've reduced it down to a...

You guys distribute a minified jsoneditor.min.js - could you please include the source map? Thanks

BGZip slow performance near end of chromosomes

3

It can take over a minute to retrieve a few bases: ``` $ time faidx --no-rebuild Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz 7:117199563-117199564 >7:117199563-117199564 GG real 1m8.888s user 0m31.042s sys 0m37.785s ``` Low coordinates are...

Announcing cdot: a data provider to load lots of transcripts fast

20

Hi, thanks for HGVS project, it’s great. I’ve written a data provider that has 5.5 times as many transcripts as UTA, and a REST service (>10x faster than public UTA...

Local UTA w/Postgres url throws exception: Generator didn't stop after throw

9

After following the local UTA and quick start: https://hgvs.readthedocs.io/en/stable/quick_start.html ``` from hgvs.assemblymapper import AssemblyMapper from hgvs.dataproviders import uta import hgvs.parser hgvsparser = hgvs.parser.Parser() var_c1 = hgvsparser.parse_hgvs_variant('NM_001197320.1:c.281C>T') hdp = uta.connect(db_url="postgresql://uta_admin:uta_admin@localhost/uta/uta_20180821") variantmapper...

Django 4.1 requires_system_checks must be a list or tuple

1

Fix for issue #112

Changelog says: Support for using a boolean value in [BaseCommand.requires_system_checks](https://docs.djangoproject.com/en/4.1/howto/custom-management-commands/#django.core.management.BaseCommand.requires_system_checks) is removed. The management command current fails with: ``` $ python3 manage.py collectstatic_js_reverse Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/django/core/management/__init__.py",...

pypi version out of date

1

The issue you fixed: https://github.com/joeribekker/django-logdb/commit/6815f48b531290857601f90b35f79ee65498df6b Has become an error rather than a deprecation since 1.4 Can you please update the pipy package to the latest Github source? Thanks.

Need to specify you only support restricted DAG - single parents only

1

Hi, your project looks nice, I needed to get method signatures so I ended up modifying it to pass in a dictionary eg: signatures = {"notify_payment" : notify_payment.si("1")} and get...

GRCh38 is the most current human reference genome, and is likely seen as the default in 2022 There is no mention in the initial README about using GRCh38 branch, this...