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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Summary
rustar-aligner-longbinary (STAR's STARlong: identical CLI, forces the chaining-DP long-read stitcher viaParameters::long_read, matching how native STAR selects it by binary rather than a flag).params.long_readthroughstitch_seeds_with_jdb_debuginto a newwindow_read_coverage(ReadAlign_stitchPieces.cpp's WC accumulation, faithful to upstream'srLast=0under-count for a seed starting at read position 0) and gate thewinReadCoverageRelativeMin/winReadCoverageBasesMincluster filter onlong_read, since standard STAR does not filter clusters by seed coverage.docs-old/dev/porting-from-star-rs.md.Test plan