fix: --batch-bytes limits sequence data size, not inflated cost#26
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… estimate The batch partitioning had a 100MB fixed overhead in its cost model, so --batch-bytes 50m would put every genome in its own batch (since the overhead alone exceeded the limit). Now --batch-bytes simply controls the maximum basepairs of sequence data per batch, which works uniformly for both FastGA and wfmash. Removed unused cost model constants (FASTGA_OVERHEAD_BYTES, WFMASH_BYTES_PER_BP, etc.), BatchLimits struct, estimate_* functions, and the estimate_cost/resource_label/auto_limit trait methods.
git describe output changes without any file changing, so Cargo
doesn't re-run build.rs and the cache key goes stale. The new key
is {version}_f{fastga_rev}_w{wfmash_rev}, parsed from Cargo.lock.
This only changes when Cargo.lock changes, which is already a
rerun-if-changed trigger.
wfmash-rs build.rs checks for PORTABLE, not WFMASH_PORTABLE. The wrong name meant wfmash was always compiled with -march=native, causing SIGILL crashes when rust-cache restores binaries built on a runner with different CPU features. Also bumps cache prefix to invalidate stale non-portable binaries.
- Add samtools faidx calls to create .fai indexes for synthetic FASTA files (required since avg_seq_len_from_fai is called unconditionally) - Add --aligner fastga to all tests in fastga_integration.rs (they were using the default wfmash aligner despite being FastGA tests) - Use larger synthetic sequences in test_thread_parameter (64bp was too small even for wfmash's minimum 100bp segment length)
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Summary
--batch-bytes 50mnow means "50 MB of sequence data per batch" instead of being compared against a cost model with a 100 MB fixed overhead that made every genome exceed the limitFASTGA_OVERHEAD_BYTES,WFMASH_BYTES_PER_BP,BatchLimits,estimate_index_size,estimate_memory_usage,resolve_batch_bytes, andestimate_cost/resource_label/auto_limittrait methods (-224 lines)--aligner fastgaand--aligner wfmashTest plan
--batch-bytes 50mwith multi-genome FASTA groups genomes into batches (not one per batch)