Welcome to Aldy’s documentation!

Contents:

• Algorithm details
• ⚠️ Warning
• Installation
  • Prerequisite: ILP solver
• Sanity check
• Running
  • Sequencing profile selection
• Output
  • VCF support
  • Problems & Debugging
• Sample datasets
• License
• Parameters & Usage
  • NAME:
  • SYNOPSIS:
  • OPTIONS:
    • Global arguments:
    • Commands:
• Gene Support
• Change log
• Acknowledgments
• Contact & Bug Reports
• API Tutorial
  • One-step genotyping API
  • Loading a gene
  • Loading a SAM/BAM or VCF file
  • Detecting copy number configurations and fusions
  • Calling the major and minor star-alleles
• Database Specification
  • Caveats
  • YAML specification
• API documentation
  • Major modules
    • aldy.gene module
    • aldy.profile module
    • aldy.sam module
    • aldy.coverage module
  • Genotyping modules
    • aldy.genotype module
    • aldy.cn module
    • aldy.major module
    • aldy.minor module
    • aldy.diplotype module
  • Auxiliary modules
    • aldy.common module
    • aldy.lpinterface module

Indices and tables

• Index
• Module Index
• Search Page