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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
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LocatePattern Functionality Overview
The obialign.LocatePattern function implements a local alignment algorithm to find the best approximate match of a short DNA pattern (e.g., primer) within a longer biological sequence, using dynamic programming.
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Input:
id: identifier for logging/error reporting.pattern []byte: the query sequence (e.g., primer).sequence []byte: the target read/contig.
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Constraints:
- Pattern must be strictly shorter than the sequence (
len(pattern) < len(sequence)).
- Pattern must be strictly shorter than the sequence (
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Scoring Scheme:
- Match:
+0(using IUPAC compatibility viaobiseq.SameIUPACNuc). - Mismatch/Gap:
-1.
- Match:
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Algorithm Features:
- End-gap free alignment (no penalty for gaps at sequence ends), enabling flexible primer positioning.
- Uses a flattened buffer (
buffIndex) for memory-efficient matrix storage (width × height). - Tracks alignment path via
patharray: diagonal (0, match/mismatch), up (+1, deletion in pattern/left gap), left (-1, insertion/deletion). - Backtracks from the bottom-right to find optimal local alignment start/end coordinates.
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Output:
start: starting index insequence.end+1: ending index (exclusive) of best match.- Error count:
-score, i.e., number of mismatches/gaps in alignment.
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Use Case:
Designed for high-throughput amplicon processing (e.g., primer trimming in metabarcoding pipelines like OBITools4).