obitools4/autodoc/docmd/pkg/obitools/obipairing/options.md

obipairing Package Functional Overview

The obipairing package provides command-line interface (CLI) support and core logic for paired-end read merging in NGS data processing. It defines configuration options, input parsing, and alignment parameters used to merge forward and reverse sequencing reads into consensus sequences.

Key Features

• Input Handling: Accepts paired FASTQ/FASTA files via --forward-reads (-F) and --reverse-reads (-R) flags.
• Alignment Parameters:
  • _Delta: Extra overlap buffer (default: 5) for refining alignment after fast detection.
  • _MinOverlap: Minimum overlap length required (default: 20).
  • _MinIdentity: Minimal sequence identity threshold for valid overlaps (default: 90%).
  • _GapPenalty: Multiplier for gap penalties relative to mismatch scores (default: 2.0).
  • _PenaltyScale: Global scaling factor for scoring (default: 1.0).
• Alignment Modes:
  • Fast heuristic alignment enabled by default (--exact-mode disables it).
  • Optional absolute scoring in fast mode via --fast-absolute.
• Output Control:
  • Statistics (e.g., overlap length, identity) can be excluded from consensus headers using --without-stat.
• Integration:
  • Extends generic input/output options from obiconvert for unified pipeline compatibility.
• Core Functions:
  • CLIPairedSequence(): Reads and pairs forward/reverse sequences.
  • Getter functions (CLI*) expose parsed parameters for downstream alignment/merging logic.

This module serves as the configuration and orchestration layer before actual sequence overlap detection, alignment scoring, and consensus generation.