elimuinformatics/vcf2hl7v2

vcf2hl7v2: a utility to convert VCF files into HL7 V2 format for genomics-EHR integration

vcf2hl7v2's Issues

Change sourceClass from required to optional

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• [ x] I am running the latest version
• [ x] I checked the documentation and found no answer
• [ x] I checked to make sure that this issue has not already been filed

Current behavior

sourceClass defaults to 'germline' and is a required field

Desired behavior

remove sourceClass default, and make it an optional field.

Documentation for vcf2hl7v2

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

Add documentation for vcf2hl7v2.

• Manual.md
• QUICKSTART.rst
• README.md
• CHANGELOG.md

Consider major allele for Homoplasmic vs Heteroplasmic

Prerequisites

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

Consider both, ALT allele depth and REF allele depth and use the major allele for Homoplasmic vs Heteroplasmic.

Current Behavior

We consider only ALT allele depth for Homoplasmic vs Heteroplasmic

Setup Dependabot for dependency updates

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

Set up dependabot for automatic dependency updates.

Current Behavior

Dependency update is not considered.

Update installation guide once published to PyPI

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

Context

The current installation guide points to the test PyPI URL. We need to update the installation guide when we release vcf2hl7v2 on PyPI.

• Package Version: latest
• Operating System: macOS

Expected Behavior

Update the installation guide when we release vcf2hl7v2 on PyPI.

Current Behavior

Installation guide points to the test PyPI URL.

Add support for the conversion of Structural Variants

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

Add support for the conversion of Structural Variants.

Current Behavior

The current code supports the conversion of simple variants (SNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.

Alternate way to populate the Gene Studied OBX

Prerequisites

Please answer the following questions for yourself before submitting an issue.

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

The file(geneKB_Gene_table.csv) is too large to be submitted with the binary. Think of a way to optimize the usage of this file or an alternate way to populate the Gene Studied OBX.

Current Behavior

The current code uses the gene geneKB_Gene_table.csv to populate the Gene Studied OBX.