fix(output): move pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab#44
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pinin4fjords wants to merge 2 commits into
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fix(output): move pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab#44pinin4fjords wants to merge 2 commits into
<prefix>_STARpass1/SJ.out.tab#44pinin4fjords wants to merge 2 commits into
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STAR writes three log files alongside Log.final.out and keeps two-pass intermediates in <prefix>_STARpass1/. rustar was only writing Log.final.out and emitting the pass-1 SJ tab as <prefix>SJ.pass1.out.tab at the top level. Add minimal Log.out (parameters dump + per-phase timestamps) and Log.progress.out (timestamp + mapping speed) writers next to the existing Log.final.out writer. Move the pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab and mkdir the parent first. The Log.out content is intentionally a stub matching the file's existence rather than STAR's full verbosity; that's a follow-up. Fixes scverse#28 Co-Authored-By: Claude <noreply@anthropic.com>
The previous commit added writers that mimicked STAR's section-header structure with placeholder content (a Debug-format params dump + three timestamps for Log.out, a header + final-timestamp line for Log.progress.out). That closes the file-existence gap but makes the output look like STAR-equivalent verbose logging when it isn't — downstream tools parsing for memory usage, per-chunk progress, or warnings would silently get nothing. Drop the stub writers. The SJ.pass1.out.tab → <prefix>_STARpass1/SJ.out.tab placement fix stays — that's a real path-parity change with no fakery. Real STAR-equivalent Log.out / Log.progress.out content (per-phase progress, warnings, memory, periodic updates during long runs) is a separate engineering effort, not a stub. Co-Authored-By: Claude <noreply@anthropic.com>
pinin4fjords
changed the title
Log.out, Log.progress.out, and <prefix>_STARpass1/SJ.out.tab<prefix>_STARpass1/SJ.out.tab
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Verified end-to-end on macOS/aarch64 against the rebuilt fix branch (commit PE yeast +
LGTM on the scoped-down PR. |
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Summary
STAR keeps two-pass intermediates inside
<prefix>_STARpass1/with the pass-1 splice tab namedSJ.out.tabinside that directory. rustar was emitting it as<prefix>SJ.pass1.out.tabat the top level. This PR moves the file to the STAR-equivalent location.The file content is unchanged — only the path moves. The
<prefix>_STARpass1/directory iscreate_dir_all'd before the write.Test plan
<prefix>_STARpass1/SJ.out.tabexists after a--twopassMode Basicrun<prefix>SJ.pass1.out.tabdoes NOT existcargo buildcargo clippy --lib -- -D warningscargo fmt --checkcargo test --lib(383 pass) +cargo test --test alignment_features test_two_pass_mode(pass)Fixes #28