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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)
1.7 KiB
1.7 KiB
Quality Shift and Read/Write Control Module
This Go package (obidefault) provides configurable controls over quality score handling in sequence data processing (e.g., FASTQ files). It defines three global variables and corresponding accessor/mutator functions:
_Quality_Shift_Input: Input quality score offset (default:33, i.e., Phred+33/Sanger format)._Quality_Shift_Output: Output quality score offset (default:33), allowing format conversion._Read_Qualities: Boolean flag indicating whether quality scores should be parsed/processed (trueby default).
Public API
| Function | Purpose |
|---|---|
SetReadQualitiesShift(shift byte) |
Sets the quality score offset for input data (e.g., when reading FASTQ). |
ReadQualitiesShift() byte |
Returns the current input quality offset. |
SetWriteQualitiesShift(shift byte) |
Sets the quality score offset for output data (e.g., when writing FASTQ). |
WriteQualitiesShift() byte |
Returns the current output quality offset. |
SetReadQualities(read bool) |
Enables/disables reading/processing of quality scores. |
ReadQualities() bool |
Returns whether qualities are currently being read/used. |
Semantic Use Cases
- Format Interoperability: Allows seamless conversion between Phred+33 (Sanger), Phred+64, or other quality encodings.
- Performance Optimization: Disabling
ReadQualitiesskips parsing of quality strings, useful when only sequences are needed. - Centralized Configuration: Global state enables consistent behavior across modules without passing parameters.
All functions are thread-unsafe by design—intended for initialization before concurrent processing begins.