apetkau/genomics-data-index issues and pull requests

#140 - Updated readme with additional installation instructions

Pull Request - State: closed - Opened by apetkau almost 2 years ago - 3 comments

#139 - Fixed up import of default node style

Pull Request - State: closed - Opened by apetkau almost 2 years ago

#138 - Fix/xorg qt ete3

Pull Request - State: closed - Opened by apetkau almost 2 years ago

#137 - Moved project metadata into toml

Pull Request - State: closed - Opened by apetkau almost 2 years ago

#136 - Update/seqproxy direct

Pull Request - State: closed - Opened by apetkau about 2 years ago

#135 - Updated conda environments to use gdi 0.8.0

Pull Request - State: closed - Opened by apetkau about 2 years ago

#134 - Removed restriction on version of sourmash

Pull Request - State: closed - Opened by apetkau about 2 years ago

#133 - Updating CI tests

Pull Request - State: closed - Opened by apetkau about 2 years ago

#132 - Fix/snpeff

Pull Request - State: closed - Opened by apetkau about 2 years ago

#131 - Feature/update python

Pull Request - State: closed - Opened by apetkau about 2 years ago

#130 - Feature/vcfpy

Pull Request - State: closed - Opened by apetkau about 2 years ago

#129 - Switch to pip for installing Python dependencies

Pull Request - State: closed - Opened by apetkau about 2 years ago

#128 - Fix/conda and deletions unknowns

Pull Request - State: closed - Opened by apetkau about 2 years ago - 1 comment

#127 - Fixed installation and testing issues

Pull Request - State: closed - Opened by apetkau about 2 years ago - 1 comment

#126 - Fix/snpeff

Pull Request - State: closed - Opened by apetkau over 2 years ago

#125 - Issue with installation.

Issue - State: closed - Opened by ayooluwaB over 2 years ago

#124 - Added newline to writing reference bedtools

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#123 - Update defaults

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#122 - Fix/comparison speed

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#121 - Feature/features comparison unknown

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#120 - Feature/update tree visual

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#119 - Summary/unknown samples

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#118 - Updated version of htslib

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#117 - Fix/quality thresholds

Pull Request - State: closed - Opened by apetkau almost 3 years ago - 1 comment

#116 - Fixed issue with missing indels in SARS-CoV-2

Pull Request - State: closed - Opened by apetkau almost 3 years ago - 2 comments

#115 - Feature/skip existing samples

Pull Request - State: closed - Opened by apetkau almost 3 years ago

#114 - Fix/snpeff annotations

Pull Request - State: closed - Opened by apetkau about 3 years ago

#113 - Feature/tree node nosize

Pull Request - State: closed - Opened by apetkau about 3 years ago

#112 - Sometimes the incorrect snpEff effect is chosen for ORF1ab (SARS-CoV-2)

Issue - State: closed - Opened by apetkau about 3 years ago
Labels: bug, variant/mutation

#111 - Cleanup temporary files

Issue - State: open - Opened by apetkau about 3 years ago
Labels: enhancement

#110 - Feature/tree comparison

Pull Request - State: closed - Opened by apetkau about 3 years ago

#109 - Download a vcf files

Issue - State: closed - Opened by Sumayah-Binhazzaa about 3 years ago - 3 comments

#108 - Switched all steps to use conda in snakemake pipeline

Pull Request - State: closed - Opened by apetkau about 3 years ago

#107 - Switched all steps to use conda in snakemake pipeline

Pull Request - State: closed - Opened by apetkau about 3 years ago

#106 - Upgrade reading VCFs

Issue - State: closed - Opened by apetkau about 3 years ago - 1 comment
Labels: installation

#105 - Changed replacement from _ to __

Pull Request - State: closed - Opened by apetkau about 3 years ago

#104 - Feature/query general

Pull Request - State: closed - Opened by apetkau about 3 years ago

#103 - Feature/load vcf kmer

Pull Request - State: closed - Opened by apetkau about 3 years ago

#102 - Fix incorrect unknown amino-acid level HGVS features

Issue - State: open - Opened by apetkau about 3 years ago
Labels: bug, variant/mutation

#101 - Feature/deletion to alignment

Pull Request - State: closed - Opened by apetkau over 3 years ago

#100 - Fix/invalid masks

Pull Request - State: closed - Opened by apetkau over 3 years ago

#99 - Accept bed files as masks

Pull Request - State: closed - Opened by apetkau over 3 years ago

#98 - Fix restoring original MLST sample names

Issue - State: open - Opened by apetkau over 3 years ago
Labels: bug, mlst

#97 - Feature/small additions

Pull Request - State: closed - Opened by apetkau over 3 years ago

#96 - Feature/split single file

Pull Request - State: closed - Opened by apetkau over 3 years ago

#95 - Fix/sample names extra characters

Pull Request - State: closed - Opened by apetkau over 3 years ago

#94 - More tests for building tree

Issue - State: open - Opened by apetkau over 3 years ago
Labels: enhancement, variant/mutation

#93 - Added Type to features_summary and features_comparison and more configurable tree generation

Pull Request - State: closed - Opened by apetkau over 3 years ago

#92 - Feature/query batcher

Pull Request - State: closed - Opened by apetkau over 3 years ago

#91 - Feature/features comparison

Pull Request - State: closed - Opened by apetkau over 3 years ago

#90 - Use existing reference sequence databases (seqrepo and snpeff)

Issue - State: open - Opened by apetkau over 3 years ago
Labels: enhancement, variant/mutation

#89 - Fixes 0.2.0

Pull Request - State: closed - Opened by apetkau over 3 years ago

#88 - Release/0.2.0

Pull Request - State: closed - Opened by apetkau over 3 years ago

#87 - Feature/sequence typer

Pull Request - State: closed - Opened by apetkau over 3 years ago

#86 - Feature/insert new data

Pull Request - State: closed - Opened by apetkau over 3 years ago

#85 - Fixing up bcftools commands to not miss variants

Pull Request - State: closed - Opened by apetkau over 3 years ago

#84 - Fix/empty universe

Pull Request - State: closed - Opened by apetkau over 3 years ago

#83 - Feature/refactor summary

Pull Request - State: closed - Opened by apetkau over 3 years ago

#82 - Look into different representation of sets of identifiers in database

Issue - State: open - Opened by apetkau over 3 years ago
Labels: data model

#81 - Add prefix to internal database ids

Issue - State: open - Opened by apetkau over 3 years ago
Labels: data model

#80 - Feature/summary mlst

Pull Request - State: closed - Opened by apetkau over 3 years ago

#79 - Feature/feature names

Pull Request - State: closed - Opened by apetkau over 3 years ago

#78 - Inconsistent snpeff/VCF entries

Issue - State: closed - Opened by apetkau over 3 years ago - 2 comments

#77 - Add tests for finding unknown sample sets by hgvs id

Issue - State: open - Opened by apetkau over 3 years ago
Labels: variant/mutation

#76 - Additional tests for mutations with same names

Issue - State: open - Opened by apetkau over 3 years ago
Labels: variant/mutation

#75 - Implement a SequenceTyper

Issue - State: open - Opened by apetkau over 3 years ago
Labels: enhancement, mlst, variant/mutation, kmer

#74 - Implement query language in command-line interface

Issue - State: open - Opened by apetkau over 3 years ago - 2 comments
Labels: enhancement

#73 - Feature/cli api

Pull Request - State: closed - Opened by apetkau over 3 years ago

#72 - Feature/parallel read vcf

Pull Request - State: closed - Opened by apetkau over 3 years ago

#71 - Combine together SNVs into MNVs for assemblies

Issue - State: open - Opened by apetkau over 3 years ago
Labels: variant/mutation

#70 - Color unknown sets on tree

Pull Request - State: closed - Opened by apetkau over 3 years ago

#69 - Improve run-time of aggregating features

Issue - State: closed - Opened by apetkau over 3 years ago - 2 comments
Labels: enhancement

#68 - Fix/index many unknown

Pull Request - State: closed - Opened by apetkau over 3 years ago

#67 - Cannot index many full-length genomes with unknown characters

Issue - State: closed - Opened by apetkau over 3 years ago - 1 comment
Labels: bug

#66 - Add ability to insert new data into an existing index

Issue - State: closed - Opened by apetkau over 3 years ago - 1 comment
Labels: enhancement

#65 - Add better support for MLST

Issue - State: open - Opened by apetkau over 3 years ago
Labels: enhancement, mlst

#64 - Feature/unknown nucleotides

Pull Request - State: closed - Opened by apetkau over 3 years ago

#63 - Missing/unknown and regular variants overlap

Issue - State: open - Opened by apetkau over 3 years ago
Labels: bug, variant/mutation

#62 - Feature/insert new data

Pull Request - State: closed - Opened by apetkau over 3 years ago

#61 - Pipeline/reads

Pull Request - State: closed - Opened by apetkau over 3 years ago

#60 - Assembly/snpeff

Pull Request - State: closed - Opened by apetkau over 3 years ago

#59 - Snpeff/hasa

Pull Request - State: closed - Opened by apetkau over 3 years ago

#58 - Adding snpeff annotations

Pull Request - State: closed - Opened by apetkau over 3 years ago

#57 - Add instructions for developing on Windows

Issue - State: open - Opened by apetkau over 3 years ago - 1 comment
Labels: documentation

#56 - Doc/move examples

Pull Request - State: closed - Opened by apetkau over 3 years ago

#55 - Doc/update tutorials

Pull Request - State: closed - Opened by apetkau over 3 years ago

#54 - Feature/summary features selection

Pull Request - State: closed - Opened by apetkau over 3 years ago

#53 - Using conda environments for indexing assemblies is very slow

Issue - State: open - Opened by apetkau over 3 years ago

#52 - Figure out how to draw trees in mybinder.org

Issue - State: closed - Opened by apetkau over 3 years ago - 2 comments
Labels: bug, documentation

#51 - Create conda package

Issue - State: closed - Opened by apetkau over 3 years ago - 3 comments
Labels: installation

#50 - Fix/improvements to cli

Pull Request - State: closed - Opened by apetkau over 3 years ago

#49 - Doc/tutorial index

Pull Request - State: closed - Opened by apetkau over 3 years ago

#48 - Doc/code docs

Pull Request - State: closed - Opened by apetkau over 3 years ago

#47 - Fix/kmer tree visualization

Pull Request - State: closed - Opened by apetkau over 3 years ago

#46 - Feature/cluster scoring 2

Pull Request - State: closed - Opened by apetkau over 3 years ago

#45 - Cluster scoring using a tree

Pull Request - State: closed - Opened by apetkau over 3 years ago

#44 - Feature/kmer parameters

Pull Request - State: closed - Opened by apetkau over 3 years ago

#43 - Feature/kmer tree

Pull Request - State: closed - Opened by apetkau over 3 years ago

#39 - Look more into how sourmash handles sequences with ambiguous (N) characters

Issue - State: open - Opened by apetkau over 3 years ago - 2 comments
Labels: kmer

#34 - Fix up overloaded `and` and `or` for SampleSet

Issue - State: closed - Opened by apetkau over 3 years ago - 1 comment
Labels: bug

GitHub / apetkau/genomics-data-index issues and pull requests