Ecosyste.ms: Issues

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GitHub / elimuinformatics/vcf2fhir issues and pull requests

#112 - add vcf2fhir sample_position parameter

Issue - State: open - Opened by rhdolin about 1 year ago

#111 - update sequence-phase-relationship-cs

Issue - State: open - Opened by rhdolin about 1 year ago

#110 - Conversion not returning all variant entries

Issue - State: closed - Opened by clake-deloitte over 1 year ago - 4 comments

#109 - Getting Wheel error for command pip install vcf2fhir

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

#108 - Question: how to scale up vcf2fhir

Issue - State: closed - Opened by mad-scientist-in-training over 1 year ago - 3 comments

#107 - vcf2fhir fails to install

Issue - State: closed - Opened by mad-scientist-in-training over 1 year ago - 2 comments

#106 - Bump fhirclient from 3.2.0 to 4.1.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#105 - Update vcf files to include DP Format Header

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

#104 - Update changelog and setup file for 0.1.1

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

#102 - Installation succeeds; "import vcf2fhir" fails

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

#100 - Revert "Updates Manual to show genomic-source-class as a required par…

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

#99 - Updates Manual to show genomic-source-class as a required parameter

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

#98 - variant inner end error fix and code-system update

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

#96 - Incorrect output when ALT is a multi-valued list

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

#95 - Create and add Project logo

Issue - State: open - Opened by srgothi92 almost 3 years ago

#94 - Add badges in Readme for higher visibility of project

Issue - State: open - Opened by srgothi92 almost 3 years ago

#93 - Updates changelog and setup file for v0.1.0

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

#92 - Adds documentation for Structural Variants and Clinical Annotations

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

#90 - genetic variant assessment should be 'absent' when GT=0/0

Issue - State: closed - Opened by Yun-00 about 3 years ago - 3 comments

#89 - Adds support for clinical annotations

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

#88 - Add Support for clinical annotations

Issue - State: closed - Opened by Rohan-cod about 3 years ago

#87 - Fixed documentation issue

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

#86 - Adds support for the conversion of Structural Variants

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

#85 - Added dependabot.yml configuration file

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

#84 - Setup Dependabot for dependency updates

Issue - State: closed - Opened by srgothi92 over 3 years ago

#83 - Deploy vcf2fhir on the bioconda channel

Issue - State: open - Opened by Rohan-cod over 3 years ago

#82 - Update Changelog for v0.0.1-v0.0.16

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

#81 - Updated logic for simple variant extraction

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

#80 - Switch to PEP 517 build

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 7 comments

#79 - Fixed base conversion for Conversion Region Disctionary

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 2 comments

#78 - Updated installation guide with steps for windows

Pull Request - State: open - Opened by Rohan-cod over 3 years ago

#77 - Fixed FHIR Validation errors and warnings

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 2 comments

#76 - Updated the location of pull request template

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

#75 - Update CHANGELOG for v0.0.17

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

#74 - Extract simple variants based on conversion region

Issue - State: closed - Opened by rhdolin over 3 years ago - 1 comment

#73 - conversion between 0-based and 1-based coordinate systems

Issue - State: closed - Opened by rhdolin over 3 years ago

#72 - Update setup.py for v0.0.17

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

#71 - Update CHANGELOG for v0.0.16

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 6 comments

#70 - Support vcf2fhir on windows !

Issue - State: open - Opened by srgothi92 over 3 years ago

#69 - Fixed case where conversion region is not studied

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 3 comments

#68 - Update Manual.md

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

#67 - Moved pull_request_template from docs to .github

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

#66 - Error when conversion region wasn't studied

Issue - State: closed - Opened by rhdolin over 3 years ago - 1 comment

#65 - Add files via upload

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

#64 - Add files via upload

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

#63 - Add genomic source class to variant observations

Issue - State: closed - Opened by rhdolin over 3 years ago - 4 comments
Labels: defer

#62 - Resource Warning due to the PyVCF3 library

Issue - State: open - Opened by Rohan-cod over 3 years ago - 1 comment

#61 - Adding minimum support version check for pyranges

Pull Request - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 2 comments

#60 - GitHub Action to build and publish Python package to PyPI

Issue - State: closed - Opened by Rohan-cod over 3 years ago - 3 comments

#59 - Refactored unit tests and integration tests

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 2 comments

#58 - To resolve Resource Warning : unclosed file

Issue - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 32 comments

#57 - Added a decorator to ignore 'Resource Warnings'

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 6 comments

#56 - Update documentation

Pull Request - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 3 comments

#55 - Simplifying the code

Pull Request - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 34 comments

#54 - Replaced np.float with float in 'fhir_helper.py'

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

#52 - Simplifying the code

Issue - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 9 comments

#51 - Refactored 'test_integration.py' to use 'with open() as file' syntax

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 2 comments

#50 - Refactored GitHub Actions to add PEP 8 formatting validation

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

#49 - Update Documentation

Issue - State: closed - Opened by srgothi92 over 3 years ago - 5 comments

#47 - Refactored python code so that it conforms to PEP8

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

#45 - Revert "GitHub Action to validate PEP 8 formatting against any new PR…

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

#44 - Updated CONTRIBUTING.md

Pull Request - State: closed - Opened by srgothi92 over 3 years ago - 1 comment

#43 - GitHub Community Checklist

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

#42 - GitHub Action to validate PEP 8 formatting against any new PR that is raised

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 3 comments

#41 - Meet the GitHub community checklist for public repository

Issue - State: closed - Opened by srgothi92 over 3 years ago - 5 comments

#40 - Refactored tests to separate Unit tests and Integration tests

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

#39 - Refactored python code so that it conforms to PEP8

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 12 comments

#38 - Setup Github Actions to run tests against any new PR that is raised

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 3 comments

#37 - Add support for multi-sample VCFs

Issue - State: closed - Opened by rhdolin over 3 years ago - 5 comments

#36 - Remove 'Human reference sequence assembly version' component from variant observation

Issue - State: closed - Opened by rhdolin over 3 years ago - 5 comments
Labels: good first issue

#35 - Refactor Idiomatic python

Issue - State: closed - Opened by srgothi92 over 3 years ago

#34 - Release a new version 0.0.17 with proper Changelog updates

Issue - State: closed - Opened by srgothi92 over 3 years ago - 1 comment

#32 - Setup Continuos Integration (CI)

Issue - State: closed - Opened by srgothi92 over 3 years ago

#31 - Data Type Validation for 'has_tabix' and 'ratio_ad_dp'

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 2 comments

#30 - Data Type validation for 'has_tabix' and 'ratio_ad_dp'.

Issue - State: closed - Opened by Rohan-cod over 3 years ago

#29 - mitochondrial DNA homoplasmic vs. heteroplasmic assignment #16

Pull Request - State: closed - Opened by abhishek-jain-1999 over 3 years ago - 1 comment

#28 - Added exclusion criteria, for cases where VCF CHROM is not recognized.

Pull Request - State: closed - Opened by Rohan-cod over 3 years ago - 3 comments

#27 - Fixed some minor issues

Pull Request - State: closed - Opened by srgothi92 almost 4 years ago

#26 - Should not exclude records where FILTER=PASS

Issue - State: closed - Opened by rhdolin almost 4 years ago

#25 - Fatal error if FORMAT.PS is missing

Issue - State: closed - Opened by rhdolin almost 4 years ago

#22 - added changes by manual to docs

Pull Request - State: closed - Opened by LondheShubham153 almost 4 years ago

#19 - Graceful handling of unknown chromosome

Issue - State: closed - Opened by rhdolin almost 4 years ago

#18 - Shift the build process to PEP-517

Issue - State: closed - Opened by rhdolin almost 4 years ago - 7 comments

#16 - mitochondrial DNA homoplasmic vs. heteroplasmic assignment

Issue - State: closed - Opened by rhdolin almost 4 years ago

#14 - Conform to HL7 find-subject-variants output

Issue - State: closed - Opened by rhdolin almost 4 years ago - 4 comments
Labels: defer

#13 - query liftover

Issue - State: closed - Opened by rhdolin almost 4 years ago - 2 comments

#12 - Searching for variants in Alt contigs

Issue - State: open - Opened by rhdolin almost 4 years ago - 2 comments
Labels: defer

#11 - vcf2fhir for structural variants

Issue - State: closed - Opened by rhdolin almost 4 years ago

#10 - added ReadTheDocs to README.md

Pull Request - State: closed - Opened by LondheShubham153 almost 4 years ago

#8 - Read the docs changes

Pull Request - State: closed - Opened by LondheShubham153 almost 4 years ago

#5 - Remove design doc files

Pull Request - State: closed - Opened by LondheShubham153 about 4 years ago