mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
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)
27 lines
1.7 KiB
Markdown
27 lines
1.7 KiB
Markdown
# 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 (`true` by 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 `ReadQualities` skips 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.
|