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Pull requests: sanjaynagi-eit/plassembler
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perf(long): pipe minimap2 straight into the plasmid FASTQ extraction (removes the last SAM in long mode)
#8
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(sam_to_fastq): take FASTQ fields from the raw SAM record (7.2x faster)
#7
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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fix: unreachable chromid warning, shared mutable defaults, unclosed bed file handles
#6
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(concat): block-copy concatenation instead of SeqRecord round-trip (89x faster, -2.6 GB)
#5
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(mash): select tophits with one groupby, de-duplicate PLSDB handling (-316 lines)
#4
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(mapping): pipe minimap2 straight into samtools sort (removes ~1.3 GiB of disk traffic per mapping)
#3
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(qc): compress chopper output with bgzip (8x faster QC stage) + wait on every pipeline stage
#2
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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perf(depth): stream samtools depth into numpy arrays (6.3x faster, -133 MB)
#1
opened Aug 13, 2026 by
sanjaynagi-eit
Owner
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