hairpin2

Contents:

  • Quickstart
    • Installation
    • Usage
    • Command Line Interface
    • hp2-utils
      • explain-var
      • get-params
  • Guide
    • Rationale, Assumptions & Limitations
    • 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
    • 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
  • hairpin2 package
  • infrastructure package
  • View page source

infrastructure package

Submodules

  • cli module
    • JSONOrFile
    • ConfigFile
  • configure_funcs module
    • make_read_processor()
    • make_variant_flagger()
  • process module
    • ReadAwareProcessProtocol
    • ReadAwareProcess
  • process_engines module
    • ProcessEngineProtocol
    • ReadTaggerEngine
    • VariantFlaggerEngine
    • ProcessKindEnum
  • process_params module
    • FixedParams
    • RunParams
  • rascheduler module
    • ConfigError
    • ExecutorError
    • ProcessError
    • RAExec
  • structures module
    • DataExtensionBase
    • record_operation()
    • mark_ext_obj()
    • ext_obj_has_mark()
    • ExtendedRead
    • make_extended_read()
    • mark_read()
    • read_has_mark()
    • ExtendedVariant
    • ReadView
    • TestOutcomes
    • FlagResult
    • ResultPackProtocol
    • VariantTestProtocol
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