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