biocommons biocommons.seqrepo issues

biocommons / biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

Apache License 2.0

39 stars 35 forks source link

issues

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update seqrepo to use the current biocommons.example project template

#119 reece opened 1 year ago
2
112 make fastadir thread safe

#118 reece closed 10 months ago
2
Thread safety for FastaDir file handle cache

#117 theferrit32 closed 10 months ago
3
rename repo

#114 ahwagner closed 7 months ago
4
Add sequence-level annotations

#113 ahwagner closed 1 year ago
3
Make FastaDir thread safe

#112 theferrit32 closed 10 months ago
9
docs: proposing to use default issue templates (#110)

#111 holtgrewe closed 1 year ago
0
style: apply style black, flake8, isort (#108)

#109 holtgrewe closed 6 months ago
4
Make coding style consistent with hgvs / enforce black and pylint

#108 holtgrewe opened 1 year ago
3
ci: update GitHub actions CI and add release-please (#104)

#107 holtgrewe closed 6 months ago
3
Remove namespace warning

#106 holtgrewe opened 1 year ago
3
Fix tests in CI

#105 holtgrewe closed 1 year ago
3
Proof of concept for release-please in biocommons.seqrepo

#104 holtgrewe opened 1 year ago
2
Suggestion: Build Ensembl transcript sequences by concatenating genomic exons

#103 davmlaw opened 1 year ago
3
Update README.md

#102 holtgrewe closed 1 year ago
0
suggestions for some changes to the existing github actions

#101 bmrobin closed 2 years ago
2
Create cqa.yml

#100 reece closed 2 years ago
1
docker build fails on Jinja2 package compatibility error

#99 bmrobin closed 2 years ago
1
Working on adding support for dataproxy

#98 andreasprlic closed 2 years ago
8
Look into improving genomic query times

#97 korikuzma closed 6 months ago
5
Cache SQLite DB lookups for seqinfo and seqid to speed up future queries

#96 joesolly closed 3 years ago
2
Empty description in setup

#95 ok-gitr closed 3 years ago
4
RFC: How to handle sequence casing and other transformations

#94 reece opened 3 years ago
3
Unable to get the data '2021-01-05' in seqrepo.

#93 git4waki closed 3 months ago
3
Add support for derived sequences

#92 reece closed 2 years ago
1
Identifiers cleanup

#91 reece opened 3 years ago
2
Re-implement support for INSDC identifiers

#90 reece opened 3 years ago
2
Implement sequence prefetching with in-memory cache

#89 reece opened 3 years ago
3
Reimplement SequenceProxy

#88 reece closed 4 years ago
0
Add info for pypi documentation

#87 reece closed 5 months ago
3
Deprecate fetch_aliases

#86 reece closed 4 years ago
0
ssl certs for dl.biocommons.org

#85 crutching closed 4 years ago
3
Add check constraints in DB schema

#84 reece opened 4 years ago
4
Reject whitespace in aliases on loading and fix existing db

#83 reece closed 4 years ago
0
Add `sha512t24us` namespace to seqrepo

#82 reece closed 4 years ago
0
Drop support for `gi` and `genbank` and remove from db

#81 reece closed 4 years ago
0
Require Ensembl aliases to be versioned and drop unversioned from database

#80 reece closed 4 years ago
0
Create mechanism to modify/fix existing databases in place

#79 reece closed 4 years ago
1
Move defline parsing to separate fx and add tests

#78 reece closed 4 years ago
0
Provide a mechanism to create release notes for a data release from logged changes

#77 reece opened 4 years ago
3
Fix alias parsing and release fixed database

#76 reece closed 4 years ago
0
Require that the `master` directory exists before loading

#75 reece closed 4 years ago
0
Update instance regexp in cli.py for 2020!

#74 reece closed 4 years ago
0
Incomplete sequence data with the 2019-09-19 release

#73 izcram closed 4 years ago
4
OSError: Unable to open SeqRepo directory /projects00/tmp/usr/hgvs/bin/seqrepo/latest

#72 ypchan closed 4 years ago
1
Provide range checking and negative coordinates a la Python

#71 reece closed 6 months ago
4
Support circular sequences

#70 reece opened 5 years ago
4
Ncbi fasta header fix

#69 andreasprlic closed 5 years ago
1
FIx documentation URLs

#68 sampearl closed 5 years ago
2
SeqRepo Query Produces KeyError (namespace not unique)

#67 akeeeshi closed 5 years ago
2

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