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fix(sam): STAR's header text, from @HD VN:1.4 to the @CO command line - #297
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STAR hard-codes `@HD VN:1.4` (samHeaders.cpp:94); rustar wrote noodles' default 1.6, so the first header line differed from STAR's in every SAM and BAM. A VN given in --outSAMheaderHD now sets the version instead of being stored as an extra field. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This was referenced Oct 8, 2026
…outSAMheaderHD - STAR builds the sorted header as samHeaderHD + "\tSO:coordinate" (samHeaders.cpp:100), so a user @hd keeps its field order and SO comes last. '-' is STAR's default for --outSAMheaderHD and was rejected as a malformed field. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…file, user @hd, transcriptome BAM STAR's header layout (samHeaders.cpp): @hd as the user wrote it (VN:1.4 by default, no VN added to a user @hd), @sq, user @pg, program @pg, comment-file lines verbatim (blank lines skipped), @rg, then @co user command line. The transcriptome BAM carries only @sq and @rg. The text is rendered once from the parameters and shared by the SAM and BAM writers. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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STAR's SAM/BAM header, line for line (started as
@HD VN:1.4, extended after review).Finding
Headers differed from STAR 2.7.11b in four ways: no
@CO user command lineline;--outSAMheaderCommentFilelines got a second@CO\tprefix;Aligned.toTranscriptome.out.bamcarried@HDand@PG; a user--outSAMheaderHDwithoutVNgotVN:1.4added; and the line order was @hd @sq @rg @pg @co instead of STAR's.Cause and fix
samHeaders.cpp:samHeaderswrites @hd, @sq, user @pg (outSAMheaderPG), program @pg, comment-file lines verbatim (blank lines skipped), @rg,@CO\tuser command line: <commandLine>. The transcriptome BAM header is @sq and @rg only (top of the same function).Parameters.cppbuildscommandLineas argv joined by spaces, a value argument with white space wrapped in quotes.The header text is now rendered once by
io::sam::render_header_text(kinds Main, MainSorted, Transcriptome) and used by the SAM, BAM, sorted BAM and stdout writers, instead of noodles' serializer. The user@HDstring is emitted verbatim, so noVNis invented (the noodles map is no longer the source of the @hd line).Parameters::star_command_lineholds STAR's command line format. The@PGID/PN/VN/CL stay rustar-aligner's own (intended difference).Results
Full headers compared with STAR on the yeast index (SAM, BAM Unsorted, BAM SortedByCoordinate, TranscriptomeSAM, with RG line,
--outSAMheaderPG, comment file,--outSAMheaderHDwith and without VN): identical apart from the program @pg line and the binary path in @co.Tests
New
header_text_follows_stars_layout; sorted-header test uses the new renderer;tests/determinism.rsalso drops@CO(it records the thread count). cargo test --release, clippy -D warnings, fmt clean.Earlier commits in this PR
@HD VN:1.4by default (samHeaders.cpp:94),SO:coordinateappended after the user's@HDfields for sorted BAM,--outSAMheaderHD -accepted as STAR's default.Part of #298.
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