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When many workers run in parallel, cnpy::npz_save opened/closed the file and rewrote the ZIP central directory 8 times per chunk, allocating ~80 MB each call. This triggered page-fault storms serialized on the per-process mmap_lock. NpzFileSession writes all 8 arrays in one fopen/fclose cycle and reuses caller-owned scratch buffers across chunks, reducing page faults to the first chunk per worker. Output is byte-compatible with numpy.savez_compressed. Signed-off-by: donghyuk <donghyuk@genome4me.com>
This reverts commit 125c3ec.
When many workers run in parallel, cnpy::npz_save opened/closed the file and rewrote the ZIP central directory 8 times per chunk, allocating ~80 MB each call. This triggered page-fault storms serialized on the per-process mmap_lock. NpzFileSession writes all 8 arrays in one fopen/fclose cycle and reuses caller-owned scratch buffers across chunks, reducing page faults to the first chunk per worker. Output is byte-compatible with numpy.savez_compressed. Signed-off-by: donghyuk <donghyuk@genome4me.com>
The consistency-mode (-C) path went through BamReader::process_read, which historically applied BAM_FUNMAP / l_qseq==0 safety checks but ignored args.filter_flag. The normal-mode (no-C) path applied `flag & args.filter_flag` in MergedDataWorker::convert_bam1_to_record. The default --filter-flag of 276 (UNMAP|REV|SEC) is applied in no-C but ignored in -C. On calls_sorted.bam this caused no-C to drop 3,127,869 reverse-strand records that -C kept. Before this commit (-C ignoring --filter-flag): -C : 543,351,974 records no-C: 540,224,105 records -> divergence of 3,127,869 reverse-strand records (REV bit 16) After this commit (-C now honors --filter-flag): -C : 540,224,105 records no-C: 540,224,105 records -> multiset-identical Signed-off-by: donghyuk <donghyuk@genome4me.com>
MergedDataWorker::convert_bam1_to_record is the per-record entry point of the normal-mode (no-C) path. It applies `flag & args.filter_flag` and an mv-tag check, but unlike the consistency-mode (-C) path's BamReader::process_read, it does NOT guard against unmapped reads or sequence-less records (l_qseq==0, the BAM-standard form for secondary alignments stored with seq='*'). The default `-g 276` (UNMAP|REV|SEC) happens to mask both via its 4 (UNMAP) and 256 (SECONDARY) bits, so default runs are safe. However, any user-supplied -g value missing those bits — e.g. -g 0, -g 4, -g 16 — lets the unsafe records through, and downstream code crashes when dereferencing the missing reference / sequence: -g 0 no-C: SIGSEGV (exit 139) -g 4 no-C: SIGSEGV (exit 139) -g 16 no-C: SIGSEGV (exit 139) -g 256 no-C: OK (l_qseq==0 records blocked via SEC bit) -g 276 no-C: OK (default) Add the same two unconditional guards that BamReader::process_read already performs on the -C path, before the existing filter_flag check: Verified on pod5_8 + calls_sorted.bam: Default --filter-flag(-g) 276: before this commit: 540,224,105 records h1=cc9e76f7ceccba4d after this commit: 540,224,105 records h1=cc9e76f7ceccba4d -> multiset-identical, no behavioural change for default users Non-default --filter-flag(-g) (10K subset, previously crashed): -g 0 before: SIGSEGV after: 1,784,476 records (filter off) -g 4 before: SIGSEGV after: 1,784,476 records (UNMAP only) -g 16 before: SIGSEGV after: 1,778,406 records (REV only) Signed-off-by: donghyuk <donghyuk@genome4me.com>
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[merger] Add BAM safety guards in normal mode
[bam] Apply --filter-flag in consistency
[npz] Single-pass NPZ writer to reduce mmap_lock contention