Allow vW:i tag for wasp in SAM output#2617
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…2687), WASP-in-SAM (alexdobin#2617), CodeQL fix (#8) * chore(release): STAR-Cross 0.0.1 versioning, main branch, CodeQL third-party exclusion - Set project/binary version to "STAR-Cross 0.0.1_<hash>" (CMakeLists + VERSION fallback); update version_check test regex to 0.0.1. - Release workflow: name releases "STAR-Cross", auto-tag fallback 0.0.1_<sha>. - CI branch triggers master -> main (codeql.yml). - CodeQL: mark cpp-httplib include as SYSTEM (CodeQL skips system headers — the reliable fix for the cpp/non-https-url alert in the #include'd httplib.h, which paths-ignore cannot filter for C/C++); broaden config globs to **/_deps/**. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * feat: allow WASP vW:i tag in SAM output (upstream PR alexdobin#2617) Emit the vW WASP filtering tag in the SAM/CRAM path and drop the BAM-only restriction on --waspOutputMode and the vW attribute. Emission is scoped to ATTR_vW only (the upstream patch incorrectly shared it with vG/vA). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * perf: multicore genomeGenerate suffix-array build (upstream PR alexdobin#2687) Port the parallel prefix-bucketed suffix-array chunk sort (with sub-binning, optional in-memory chunk retention, and a skip-first-word comparator fast-path) from upstream PR alexdobin#2687. Reconciled with the fork: - funCompareSuffixesFromWord uses the big-endian-safe loadUintLE loads. - sjdbSortBucket reformulated without __uint128 (MSVC has no native 128-bit); the bucket mapping stays monotonic in the key, so the total order — and thus the final index — is unchanged. - SA chunk packing keeps the in-memory path and the binary-mode disk fallback. Index output is byte-identical to the previous builder; a new CI job (validate-genome-index) builds the main baseline and this branch and diffs the SA/SAindex/Genome across 1 vs 16 threads and a low-RAM multi-chunk layout. build.yml CI branch triggers also move master -> main. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: STAR-Cross 0.0.1, CRAM/big-endian/ARM, genomeGenerate perf, WASP-in-SAM Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(win): use signed loop indices in OpenMP parallel-for (MSVC OpenMP 2.0) MSVC's OpenMP 2.0 requires signed integral index variables in `#pragma omp for`. The alexdobin#2687 ports used `uint` (64-bit) indices; switch the new parallel-for loops to int64 (genomeGenerate genome scans, genomeSAindex chunks, sjdbBuildIndex bucket count/scatter). No behavior change on GCC/Clang. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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…osix_spawn, WASP vW in SAM - Windows: open genome/SA/Genome files in binary mode (streamFuns). - Referenceless CRAM output (--outSAMtype CRAM) via cramOutput.cpp (CRAM_OPT_NO_REF), transcoded from BAM at finalization; hot path untouched. - macOS: spawn readFilesCommand via posix_spawnp (issue alexdobin#2663); Windows path unchanged. - Allow WASP vW:i tag in SAM/CRAM output, not just BAM (upstream PR alexdobin#2617). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Allowing wasp tags in SAM output seems straightforward (and seems to be identical after this modification to converting BAM to SAM). Maybe it was just not implemented, but I can't see any reason why such a tag would actually be problematic in SAM.
This PR only looks at a few code pathways, so probably many more tags/modes should be changed, but this addresses a common usecase.