feat: STARlong binary + long-read window-coverage filter - #116
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feat: STARlong binary + long-read window-coverage filter#116BenjaminDEMAILLE wants to merge 2 commits into
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Add rustar-aligner-long binary (STAR's STARlong: identical CLI, forces the chaining-DP long-read stitcher via Parameters::long_read, matching how native STAR selects it by binary rather than a flag). Wire params.long_read through stitch_seeds_with_jdb_debug into a new window_read_coverage (ReadAlign_stitchPieces.cpp's WC accumulation, faithful to upstream's rLast=0 under-count for a seed starting at read position 0) and gate the winReadCoverageRelativeMin/winReadCoverageBasesMin cluster filter on long_read, since standard STAR does not filter clusters by seed coverage. Refactor stitch_seeds_core's preamble into prepare_stitch_input, shared with the (upcoming) STARlong chaining-DP stitcher stitch_seeds_long_read. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
`extend_alignment` gained an `extend_to_end` argument when --alignEndsType landed. The two long-read chaining call sites pass `false`: they score a seed's own extension potential during chaining, and --alignEndsType applies at the read ends, not there. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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STARlong:
rustar-aligner-longbinary and the long-read window-coverage filter.What changed
rustar-aligner-long, mirroring STAR's STARlong: identical CLI, forcing the long-read stitcher viaParameters::long_read. Native STAR selects this by binary rather than by flag, and this matches that.window_read_coverage, STAR's WC accumulation fromReadAlign_stitchPieces.cpp, threaded throughstitch_seeds_with_jdb_debug. The--winReadCoverageRelativeMin/--winReadCoverageBasesMincluster filter is gated onlong_read, since standard STAR does not filter clusters by seed coverage.--winReadCoverageBasesMinis new;--winReadCoverageRelativeMinalready existed with default 0.5 and becomes effective.Why
This is the themed split of the original bundled WASP-and-everything PR, per
docs-old/dev/porting-from-star-rs.md.One faithful defect
window_read_coverage_matches_star_rlast_zero_undercountpins STAR'srLast = 0under-count for a seed starting at read position 0. It is reproduced rather than fixed: the filter threshold is calibrated against STAR's own numbers, so correcting the count in isolation would change which windows survive relative to the oracle.Verification
cargo build,cargo test,cargo clippy -D warnings,cargo fmt --check— all green. Rebased onto currentmain.🤖 Generated with Claude Code