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41 lines
2.4 KiB
Markdown
41 lines
2.4 KiB
Markdown
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# Semantic Description of `obingslibrary` Marker Module
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The `Marker` struct defines a molecular biology primer pair (forward/reverse) for PCR-based sample demultiplexing in high-throughput sequencing workflows. It supports flexible configuration of primer binding, tag (barcode) extraction, mismatch tolerance, and indel handling.
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## Core Functionalities
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- **Primer Pattern Compilation**:
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`Compile()` and `Compile2()` initialize forward/reverse primer patterns using the underlying `obiapat.ApatPattern`, including reverse-complement variants (`cforward`, `creverse`). They accept parameters for maximum error tolerance and indel allowance.
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- **Sequence Matching & Demultiplexing**:
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`Match()` scans a given sequence (`BioSequence`) for primer binding sites. It prioritizes forward-primer detection, then falls back to reverse if needed. For each match:
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- Extracts primer region and adjacent tag (barcode).
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- Computes mismatches.
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- Links to a pre-registered `PCR` object via the tag pair (`TagPair`) key in internal map.
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- **Sample Registration & Lookup**:
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`GetPCR()` retrieves or registers a new PCR reaction entry indexed by forward/reverse tag pair (case-insensitive). Enables tracking of sample-specific amplification data.
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- **Tag Length Validation**:
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`CheckTagLength()` ensures all registered tags have uniform length for both directions; otherwise, returns an error.
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- **Configurable Parameters**:
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Supports tuning of:
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- Tag lengths (`Forward_tag_length`, `Reverse_tag_length`)
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- Spacer between tag and primer (`SetTagSpacer()`)
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- Delimiter for tag-primer boundary (e.g., `a`, `c`, `g`, `t` or none via `'0'`)
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- Allowed mismatches and indels per primer (`SetAllowedMismatch()`, `SetTagIndels()`)
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- Matching strategy: `"strict"` (exact), `"hamming"`, or `"indel"`
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- **Matching Strategy Enforcement**:
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`SetForward/ReverseMatching()` validates and sets matching modes; invalid values raise errors.
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## Design Highlights
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- Uses `log.Fatalf` for critical configuration failures (e.g., invalid delimiter).
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- Leverages reference-counted sequences (`Recycle()`) for memory efficiency.
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- Prioritizes forward primer match but gracefully handles reverse orientation.
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- Fully supports case-insensitive tag comparison and normalization.
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This module serves as the core engine for sample assignment in amplicon-based NGS pipelines, balancing sensitivity (via error/indel tolerance) and specificity (through tag uniqueness).
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