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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)
32 lines
1.5 KiB
Markdown
32 lines
1.5 KiB
Markdown
# `Speed` Functionality Description
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The provided Go code defines a method and helper function to add **real-time progress tracking** to biosequence iterators in the OBITools4 framework.
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## Core Features
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- **Non-intrusive progress bar**:
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The `Speed()` method wraps an existing iterator and displays a visual progress indicator on stderr, using the [`progressbar`](https://github.com/schollz/progressbar) library.
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- **Conditional rendering**:
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The progress bar is only shown when:
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- `--no-progressbar` flag is *not* set (via `obidefault.ProgressBar()`),
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- stderr is connected to a terminal (`os.ModeCharDevice`),
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- stdout is *not* piped (to avoid interfering with file output).
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- **Batch-aware counting**:
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Progress is updated per batch (`batch.Len()`), not item-by-item, for efficiency and smoother UI updates (throttled to ≥100ms).
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- **Paired-end support**:
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If the input iterator is paired (`IsPaired()`), this property is preserved in the returned iterator.
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- **Pipeable wrapper**:
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`SpeedPipe()` enables integration into functional pipelines (e.g., `.Map(...).Filter(...)`) by returning a `Pipeable` function.
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## Implementation Highlights
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- Uses goroutines to decouple iteration and progress updates.
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- Automatically closes the output iterator when input ends (`WaitAndClose()`).
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- Prints a final newline to stderr upon completion.
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This utility enhances user experience during long-running sequence processing (e.g., FASTQ parsing, alignment), without affecting correctness or performance in non-interactive contexts.
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