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refactor: replace single batch size with min/max bounds and memory limits

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Introduce separate _BatchSize (min) and _BatchSizeMax (max) constants to replace the single _BatchSize variable. Update RebatchBySize to accept both maxBytes and maxCount parameters, flushing when either limit is exceeded. Set default batch size min to 1, max to 2000, and memory limit to 128 MB. Update CLI options and sequence_reader.go accordingly.
This commit is contained in:
Eric Coissac
2026-03-13 15:07:31 +01:00
parent 40769bf827
commit 1e1f575d1c
4 changed files with 38 additions and 16 deletions
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8
pkg/obioptions/options.go
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@@ -56,11 +56,15 @@ func RegisterGlobalOptions(options *getoptions.GetOpt) {
options.IntVar(obidefault.BatchSizePtr(), "batch-size", obidefault.BatchSize(),
options.GetEnv("OBIBATCHSIZE"),
options.Description("Number of sequence per batch for paralelle processing"))
options.Description("Minimum number of sequences per batch (floor, default 1)"))
options.IntVar(obidefault.BatchSizeMaxPtr(), "batch-size-max", obidefault.BatchSizeMax(),
options.GetEnv("OBIBATCHSIZEMAX"),
options.Description("Maximum number of sequences per batch (ceiling, default 2000)"))
options.StringVar(obidefault.BatchMemStrPtr(), "batch-mem", "",
options.GetEnv("OBIBATCHMEM"),
options.Description("Maximum memory per batch (e.g. 128K, 64M, 1G). Overrides --batch-size when set."))
options.Description("Maximum memory per batch (e.g. 128K, 64M, 1G; default: 128M). Set to 0 to disable."))
options.Bool("solexa", false,
options.GetEnv("OBISOLEXA"),