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Auto-clipping treats any String or Array attribute as per-base when its length equals the read's length before clipping. A read of length n whose RG ID is also n characters long therefore has its RG sliced along with its bases, leaving an ID that is not in the header. SamRecordClipper now skips the SAM tags that are never per-base: RG, LB, PU, PG, CO, MI, the sample, cell and molecular barcode tags with their qualities, and MC, SA, OA and OC. MD, NM and UQ are already invalidated by clipping.
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This bit me because it was clipping my read group ID! Wild bug. It also went silent for some time since many downstream tools only warn for read groups not in the header, not halt. |
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Copilot review overview
🟡 Changes recommended
The protected set omits SAM fields that generic slicing can corrupt, and the self-derived test cannot detect such omissions.
Review effort: Balanced
Findings: 1
Open (2)
What changed in this PR
Prevents auto-clipping from corrupting non-per-base SAM tags, mirroring the fgumi fix.
Changes:
- Adds a protected-tag set to clipping logic.
- Documents exceptions in CLI options.
- Adds regression coverage.
| File | Description |
|---|---|
SamRecordClipper.scala |
Skips protected tags during auto-clipping. |
SamRecordClipperTest.scala |
Tests protected and per-base tags. |
ClipBam.scala |
Updates option documentation. |
TrimPrimers.scala |
Updates option documentation. |
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Included review availability: This review used your included allowance. Your plan provides up to 2 included reviews per hour; 1 remain after this review. 📝 WalkthroughWalkthroughThe clipper now skips tags listed in Priority: ➖ Normal Merge Risk: ⚪ Minimal · up to No actionable merge-blocking risk remains in the reviewed change; it is mergeable after normal checks. Security Architecture ReviewSecurity architecture risk: 🔵 Low · up to The change does not introduce new access or privileges. Its main risk is that preserved base-modification metadata can become inconsistent with a shortened read and propagate to downstream readers. Retained concerns
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R2 and Q2 hold the mate's sequence and qualities, so with equal-length mates they match the read's length and were sliced with the wrong read's clip coordinates. CC, CT, FS, PT and FZ are structured values, not per-base data. The test now lists the protected tags itself and checks the set against it, so dropping a tag fails the test.
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Actionable comments posted: 1
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Inline comments:
Review comments at
@src/main/scala/com/fulcrumgenomics/bam/SamRecordClipper.scala:
- Around line 57-64: Update the hard-clipping behavior in ClipBam so
autoClipAttributes=true does not leave MM/ML annotations for removed bases;
recalculate them for the clipped sequence or invalidate them. Adjust
TagsNeverAutoClipped as needed so excluding these tags does not preserve stale
annotations.
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📒 Files selected for processing (4)
src/main/scala/com/fulcrumgenomics/bam/ClipBam.scalasrc/main/scala/com/fulcrumgenomics/bam/SamRecordClipper.scalasrc/main/scala/com/fulcrumgenomics/bam/TrimPrimers.scalasrc/test/scala/com/fulcrumgenomics/bam/SamRecordClipperTest.scala
🚧 Files skipped from review as they are similar to previous changes (2)
- src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala
- src/main/scala/com/fulcrumgenomics/bam/TrimPrimers.scala
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CG holds the real CIGAR of alignments with more than 65,535 operations, so a matching-length array was sliced like per-base data. The ClipBam and TrimPrimers help now names RG as the only example of the listed tags.
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Doc test blocked by: #1183 |
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Two things, mirroring fulcrumgenomics/fgumi#1019:
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MD is not per-base data, and the soft-to-hard upgrade path auto-clips without invalidating it, so a still-valid MD whose length equals the read's was sliced there. XA (bwa), cs (minimap2), jM/jI (STAR), GX/GN (STARsolo, Cell Ranger), BX (linked reads) and dorado's mv/pi/st/fn are not per-base either. The shared tags now match fgumi's list. The list is documented as best-effort. The test now runs on the upgrade path, so MD is exercised, and checks that real per-base tags (OQ, E2 and a cd array) are still clipped.
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Both done in dfc76e2.
I also mirrored the rest of the fgumi review: the doc now says the list is best-effort, and the test runs on the upgrade path and checks that real per-base tags ( |
--auto-clip-attributes(ClipBam, and-ainTrimPrimers) clips any String or Array attribute whose length equals the read's length before clipping (SamRecordClipper.clipExtendedAttributes). That length test can't tell a per-base tag from an identifier that happens to be as long as the read.What goes wrong
A read of length
nwhoseRGID is alsoncharacters long has itsRGhard-clipped exactly like its bases. Clippingkbases leaves anRGofn - kcharacters, an ID that is not in the header, so strict validation fails and lenient readers warn per record.MI,RX,CB,SAand the other non-per-base tags are exposed the same way.The fix
SamRecordClipper.TagsNeverAutoClippedlists tags that are never per-base, and auto-clipping skips them:RG,LB,PU,PG,CO,MIBC,QT,RX,QX,OX,BZ,CB,CR,CY,UB,UR,UY,BXMC,MD,SA,OA,OC,CG,XA(bwa),cs(minimap2),jM/jI(STAR)CC,CT,FS,PT,GX/GN(STARsolo, Cell Ranger)R2,Q2(equal-length mates match the read's length all the time)FZ,MM,ML, and dorado'smv,pi,st,fnThe list is best-effort: an unlisted tag whose length matches the read's is still clipped.
MDis listed because the soft-to-hard upgrade (upgradeClipping) auto-clips without invalidating it, so a still-validMDcould be sliced there;NMandUQare integers, which auto-clipping never touches.The test pins the set, runs on the upgrade path so
MDis exercised, and checks that real per-base tags (OQ,E2, acdarray) and an unlisted one are still clipped. TheClipBamandTrimPrimersoption docs now name the exception.fulcrumgenomics/fgumi has the same flaw; the matching fix is fulcrumgenomics/fgumi#1019. Both lists hold the same tags apart from each tool's own: fgumi also protects its
obandtc, and guardsMM/MLin a separate base-modification check.