Description

qannotate previously enforced a single -mode per run, requiring repeated load/annotate/write cycles for multi-step annotation workflows. This change allows multiple modes to be specified and executed sequentially in one CLI invocation while preserving existing single-mode behavior.

• CLI parsing: multi-mode support

  • Options captures all provided --mode values (getModes()), while retaining getMode() (first mode) for compatibility.
  • Mode-specific argument registration (eg. -d, --config, --summaryFile, --test/--control) is enabled when any selected mode requires it.

• Execution flow: chained per-mode runs

  • Main now branches on options.getModes():
    • single mode: unchanged path
    • multiple modes: execute modes in order, piping intermediate output through temp VCFs and writing final output once
  • Added explicit guard to reject multi-mode runs containing vcf2maf/vcf2maftmp in mixed pipelines.

• Per-mode database assignment in multi-mode runs

  • Multi-mode execution now extracts all -d/--database arguments once and assigns them in order to only the modes that require a database.
  • Modes that do not require a database do not consume a -d.
  • Supports -d value, -d=value, and --database=value forms when collecting database arguments.

• Focused tests

  • Added OptionsTest.multipleModes() to verify ordered multi-mode parsing and backward-compatible primary mode behavior.
  • Added/updated MainTest coverage for:
    • per-mode argument rewriting with explicit per-mode database inputs
    • ordered extraction of database arguments

// supported: ordered modes, ordered per-mode databases for database-requiring modes
qannotate --mode dbsnp --mode confidence --mode germline -i in.vcf -o out.vcf -d dbsnp.vcf -d germline.vcf

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Targeted qannotate unit tests were run for multi-mode parsing, per-mode argument rewriting, and database argument handling.

• au.edu.qimr.qannotate.OptionsTest
• au.edu.qimr.qannotate.MainTest

Are WDL Updates Required?

No WDL updates required; change is isolated to qannotate CLI option parsing/execution flow.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

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