Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / zavolanlab/htsinfer issues and pull requests

#172 - docs: update RtD guides

Pull Request - State: closed - Opened by balajtimate 24 days ago - 2 comments

#171 - refactor: update logging level

Pull Request - State: closed - Opened by balajtimate about 1 month ago - 1 comment

#170 - perf: use estimated counts instead of TPM

Pull Request - State: closed - Opened by balajtimate about 1 month ago - 1 comment

#169 - feat: output read orientation fractions to json

Pull Request - State: closed - Opened by balajtimate about 2 months ago - 3 comments

#168 - refactor: update transcript list

Pull Request - State: closed - Opened by balajtimate about 2 months ago - 4 comments

#167 - Error using zarp-cli

Issue - State: open - Opened by MSaadfarooq 6 months ago - 1 comment

#166 - perf: update regex for seqid

Pull Request - State: closed - Opened by balajtimate 7 months ago - 1 comment

#165 - fix: seqid with dash not matching regex

Issue - State: closed - Opened by balajtimate 7 months ago

#164 - build: add data dir to MANIFEST.in

Pull Request - State: closed - Opened by balajtimate 10 months ago - 2 comments

#163 - build: create data package

Pull Request - State: closed - Opened by balajtimate 10 months ago - 3 comments

#162 - refactor: pre-release cleanup

Pull Request - State: closed - Opened by balajtimate 10 months ago - 1 comment

#161 - feat: improve lib type inference for SRA PE samples

Pull Request - State: closed - Opened by balajtimate 10 months ago - 1 comment

#160 - feat: improve lib type relationship inference for SRA samples

Issue - State: closed - Opened by balajtimate 10 months ago - 3 comments

#159 - feat: sort alignments by read name

Issue - State: open - Opened by balajtimate 11 months ago
Labels: low_priority, future

#158 - refactor: reduce memory usage of comparing alignments

Issue - State: open - Opened by balajtimate 11 months ago
Labels: low_priority, future

#157 - fix: infer library type relationship

Pull Request - State: closed - Opened by balajtimate 11 months ago - 3 comments

#156 - Package and document analysis code

Issue - State: open - Opened by uniqueg 11 months ago - 1 comment

#155 - Create overview figure panel

Issue - State: closed - Opened by uniqueg 11 months ago - 8 comments

#154 - Create dataset overview tables

Issue - State: closed - Opened by uniqueg 11 months ago - 1 comment

#152 - fix: correctly infer read stats from second mate

Pull Request - State: closed - Opened by balajtimate 12 months ago - 1 comment

#151 - Compare inferred read length statistics to SRA metadata

Issue - State: closed - Opened by balajtimate 12 months ago - 1 comment

#150 - fix: add processed sample paths to mapping

Pull Request - State: closed - Opened by balajtimate about 1 year ago - 4 comments

#148 - feat: set default for records

Pull Request - State: closed - Opened by balajtimate about 1 year ago - 3 comments

#147 - feat: add tax_id parameter

Pull Request - State: closed - Opened by balajtimate about 1 year ago - 1 comment

#146 - fix: update Pydantic version

Pull Request - State: closed - Opened by balajtimate about 1 year ago - 1 comment

#145 - Publish HTSinfer on Bioconda

Issue - State: closed - Opened by uniqueg about 1 year ago - 1 comment

#144 - Unexpected errors throw same status code as warnings

Issue - State: closed - Opened by uniqueg about 1 year ago

#143 - Dockerfile does not make use of Conda environment

Issue - State: closed - Opened by uniqueg about 1 year ago

#142 - Conda-based Dockerfile & new exit status for unexpected errors

Pull Request - State: closed - Opened by uniqueg about 1 year ago - 1 comment

#141 - Fix bugs

Pull Request - State: closed - Opened by uniqueg about 1 year ago - 1 comment

#140 - Pydantic 2.0 is not supported

Issue - State: closed - Opened by uniqueg about 1 year ago

#139 - Correctly set supported Python versions

Issue - State: closed - Opened by uniqueg about 1 year ago

#138 - Warnings potentially override error state

Issue - State: closed - Opened by uniqueg about 1 year ago

#137 - fix: add default to path_2_processed arg

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#136 - test: update ci ref on docker publish

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#135 - Ci test

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#134 - test: update ci ref on docker publish

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#133 - feat: infer additional statistics from read lengths

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#132 - Expand inferred read length stats

Issue - State: closed - Opened by balajtimate over 1 year ago

#131 - refactor: avoid duplicate mappings

Pull Request - State: closed - Opened by BorisYourich over 1 year ago - 10 comments

#130 - Create Mapping class for managing STAR cmd and outputs

Issue - State: closed - Opened by BorisYourich over 1 year ago

#129 - feat: infer lib type if mate info not in seq IDs

Pull Request - State: closed - Opened by BorisYourich over 1 year ago - 5 comments

#128 - ci: publish Docker image

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#127 - feat: push docker image in ci

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#126 - feat: automatically push docker image in CI workflow

Issue - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#125 - perf: optimize STAR memory usage and read orientation defaults

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#124 - perf: optimize read layout inference and defaults

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#123 - chore: configure GitHub Codespaces for this project

Pull Request - State: closed - Opened by AngryMaciek over 1 year ago - 4 comments
Labels: enhancement, good first issue

#122 - perf: remove duplicate adapter fragments

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#121 - Remove similar adapters to increase frequency ratio

Issue - State: closed - Opened by balajtimate over 1 year ago - 3 comments

#120 - GitHub Actions takes hours

Issue - State: closed - Opened by uniqueg over 1 year ago

#119 - ci: downgrade Cutadapt & silence warning

Pull Request - State: closed - Opened by uniqueg over 1 year ago - 1 comment

#118 - Test warning for deprecated Pandas feature

Issue - State: closed - Opened by uniqueg over 1 year ago

#117 - fix: remove transcript duplicates

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 6 comments

#116 - Remove duplicates from transcripts file

Issue - State: closed - Opened by balajtimate over 1 year ago

#115 - STAR fails to create index

Issue - State: closed - Opened by balajtimate over 1 year ago - 5 comments

#114 - perf: add adapter fragment

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#113 - Look into potential uses of seqspec

Issue - State: open - Opened by balajtimate over 1 year ago - 1 comment
Labels: future

#112 - refactor: wrap long line

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 1 comment

#111 - test: design testing strategy

Pull Request - State: closed - Opened by balajtimate over 1 year ago - 2 comments

#110 - Run first tests

Issue - State: closed - Opened by balajtimate over 1 year ago - 2 comments

#109 - Optimize performance

Issue - State: closed - Opened by balajtimate over 1 year ago - 12 comments

#108 - Analyze organism/source

Issue - State: closed - Opened by uniqueg over 1 year ago - 12 comments
Labels: library source

#107 - Analyze 3' end adapters

Issue - State: closed - Opened by uniqueg over 1 year ago - 13 comments

#106 - Add missing known adapters to adapters file

Issue - State: closed - Opened by uniqueg over 1 year ago - 1 comment

#105 - Compile a list of common model organisms to retrieve test samples for

Issue - State: closed - Opened by uniqueg over 1 year ago - 1 comment

#104 - Issue 98

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

#103 - build: Docker builds without Conda

Pull Request - State: closed - Opened by BorisYourich almost 2 years ago - 1 comment

#102 - Infer polyA tail & Conda to Mamba

Pull Request - State: closed - Opened by BorisYourich almost 2 years ago - 5 comments

#101 - Change from conda to mamba in CI workflows

Issue - State: closed - Opened by BorisYourich almost 2 years ago

#100 - Populate reference data matrix

Issue - State: closed - Opened by uniqueg about 2 years ago - 10 comments

#99 - feat: infer presence of polyA tail fragments

Pull Request - State: closed - Opened by BorisYourich about 2 years ago - 6 comments

#98 - Design testing strategy

Issue - State: closed - Opened by uniqueg about 2 years ago

#97 - refactor: exception handling #94

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

#96 - Docker image for the htsinfer project

Issue - State: closed - Opened by BorisYourich about 2 years ago - 1 comment

#95 - refactor: pass conf instances, not individual args #92

Pull Request - State: closed - Opened by BorisYourich about 2 years ago - 4 comments

#94 - Handling exceptions to reduce duplicated code

Issue - State: closed - Opened by rohank63 about 2 years ago

#93 - pytest issue on macOS Big Sur

Issue - State: closed - Opened by BorisYourich about 2 years ago - 3 comments

#92 - refactor: pass conf instances, not individual args

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

#91 - test: add unit tests for library orientation

Pull Request - State: closed - Opened by rohank63 over 2 years ago - 2 comments

#90 - test: add unit tests for library source inference

Pull Request - State: closed - Opened by rohank63 over 2 years ago - 1 comment

#89 - Infer read layout generically

Issue - State: open - Opened by uniqueg over 2 years ago - 2 comments
Labels: enhancement, read layout, future

#88 - Bug fixes

Pull Request - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#87 - Support additional source naming schemes

Issue - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#86 - Infer presence of polyA tails in reads

Issue - State: closed - Opened by uniqueg over 2 years ago - 3 comments
Labels: read layout

#85 - Infer library type if sequence identifiers do not contain mate info

Issue - State: closed - Opened by uniqueg over 2 years ago - 7 comments
Labels: library type

#84 - Refactor argument passing to class instances

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

#83 - Implement unit tests for read orientation inference

Issue - State: closed - Opened by uniqueg over 2 years ago
Labels: read orientation

#82 - Implement unit tests for library source inference

Issue - State: closed - Opened by uniqueg over 2 years ago - 1 comment
Labels: library source

#81 - docs: extend main documentation

Pull Request - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#80 - build: add Dockerfile

Pull Request - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#79 - fix(orient): handle sources

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

#78 - fix(orientation): handle sources

Pull Request - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#77 - feat: calculate library statistics

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

#76 - fix(orient): handle reads with adapters

Pull Request - State: closed - Opened by uniqueg over 2 years ago - 1 comment

#75 - ci: migrate to GH Actions

Pull Request - State: closed - Opened by AngryMaciek over 2 years ago - 5 comments
Labels: enhancement

#74 - ci: move to GitHub Actions

Issue - State: closed - Opened by AngryMaciek over 2 years ago - 1 comment
Labels: enhancement, good first issue

#73 - feat: read orientation

Pull Request - State: closed - Opened by rohank63 over 3 years ago - 1 comment