hairpin2

Contents:

  • Quickstart
    • Installation
    • Usage
    • Command Line Interface
    • hp2-utils
      • explain-var
      • get-params
  • Guide
    • Processes and Parameters
      • Process Relationships Reference
      • Read Taggers
        • mark-support
        • mark-overlap
        • mark-low-qual
        • mark-duplicates
      • Variant Flaggers
        • LQF
        • DVF
        • ALF
        • ADF
    • Writing a Config
    • Understanding Decisions
    • Reproducibility & Parameter Distribution
    • Assumptions & Limitations
    • Further Development
  • hairpin2 package
    • Scientific Modules
      • const module
        • ValidNucleotides
        • Strand
        • MutTypes
        • Tags
        • TaggerNamespaces
        • FlaggerNamespaces
      • sci_funcs module
        • TagSupportingReads
        • TagLowQualReads
        • TagFragmentReads
        • TagStutterDuplicateReads
        • AlignmentScoreTest
        • AnomalousDistributionTest
        • ProportionBasedTest
      • main module
        • hairpin2()
    • Subpackages
      • infrastructure package
        • Submodules
      • process_wrappers package
        • Submodules
  • Developer Documentation
hairpin2
  • Overview: module code

All modules for which code is available

  • hairpin2.const
  • hairpin2.infrastructure.cli
  • hairpin2.infrastructure.configure_funcs
  • hairpin2.infrastructure.process
  • hairpin2.infrastructure.process_engines
  • hairpin2.infrastructure.process_params
  • hairpin2.infrastructure.rascheduler
  • hairpin2.infrastructure.structures
  • hairpin2.main
  • hairpin2.process_wrappers.ADF
  • hairpin2.process_wrappers.ALF
  • hairpin2.process_wrappers.DVF
  • hairpin2.process_wrappers.LQF
  • hairpin2.process_wrappers.mark_overlap
  • hairpin2.process_wrappers.mark_support
  • hairpin2.process_wrappers.shared
  • hairpin2.sci_funcs

© Copyright 2025, Alex Byrne.

Built with Sphinx using a theme provided by Read the Docs.