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
• Known issues and limitations
• 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
      • CNConfig
      • CNConfigType
      • Gene
      • MajorAllele
      • MinorAllele
      • Mutation
    • aldy.profile module
      • Profile
    • aldy.sam module
      • Sample
      • detect_genome()
    • aldy.coverage module
      • Coverage
  • Genotyping modules
    • aldy.genotype module
      • genotype()
    • aldy.cn module
      • estimate_cn()
      • solve_cn_model()
    • aldy.major module
      • estimate_major()
      • solve_major_model()
    • aldy.minor module
      • estimate_minor()
      • solve_minor_model()
    • aldy.diplotype module
      • OUTPUT_COLS
      • estimate_cpic()
      • estimate_diplotype()
      • write_decomposition()
      • write_vcf()
  • Auxiliary modules
    • aldy.common module
      • AldyException
      • GRange
      • JsonDict
      • PROTEINS
      • REV_COMPLEMENT
      • SOLUTION_PRECISION
      • Timing
      • allele_name()
      • chr_prefix()
      • colorize()
      • freezekey()
      • log
      • parse_cn_region()
      • pp()
      • rev_comp()
      • script_path()
      • seq_to_amino()
      • sorted_tuple()
      • td()
    • aldy.lpinterface module
      • CBC
      • Gurobi
      • NoSolutionsError
      • SOLVER_PRECISON
      • escape_name()
      • model()
• Aldy Software License Agreement

Indices and tables

• Index

• Module Index

• Search Page