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feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility #36

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feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility #36

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b8ba281
feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility
pinin4fjords May 12, 2026
9a7be3e
chore(params): trim verbose doc comment
pinin4fjords May 12, 2026
cc3e48a
chore(params): warn at runtime when --limitGenomeGenerateRAM is set
pinin4fjords May 12, 2026
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7 changes: 7 additions & 0 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,13 @@ fn genome_generate(params: &Parameters) -> anyhow::Result<()> {
.collect::<Vec<_>>()
);

if params.limit_genome_generate_ram != 31_000_000_000 {
log::warn!(
"--limitGenomeGenerateRAM {} accepted but not enforced; rustar manages genome-generation memory independently",
params.limit_genome_generate_ram
);
}

info!("Building genome index...");
let index = GenomeIndex::build(params)?;

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4 changes: 4 additions & 0 deletions src/params.rs
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Expand Up @@ -363,6 +363,10 @@ pub struct Parameters {
#[arg(long = "limitBAMsortRAM", default_value_t = 0)]
pub limit_bam_sort_ram: u64,

/// Maximum RAM (bytes) for genome generation.
#[arg(long = "limitGenomeGenerateRAM", default_value_t = 31_000_000_000_u64)]
pub limit_genome_generate_ram: u64,

/// Route primary alignment output to stdout instead of a file.
/// Values: None (default), SAM, BAM_Unsorted, BAM_SortedByCoordinate.
#[arg(long = "outStd", default_value = "None")]
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