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fix(merge): rename conflicting @RG/@PG IDs per input and rewrite read tags - #1050
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Walkthrough
ChangesMerge reconciliation
Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~45 minutes Change: Bug fix Sequence Diagram(s)sequenceDiagram
participant MergeExecute as Merge::execute
participant HeaderMerge as merge_headers
participant TagRewriter as ReadTagRewriter
participant Sorter as RawExternalSorter::merge_bams_rewriting
participant Output as BAM output
MergeExecute->>HeaderMerge: Build merged header and per-input rename maps
MergeExecute->>TagRewriter: Initialize read-tag mappings
MergeExecute->>Sorter: Pass merged header and record rewrite callback
Sorter->>TagRewriter: Rewrite each record using its input index
Sorter->>Output: Write records after sort-key extraction
Suggested labels: Merge Risk: ⚪ Minimal · up to
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Review comments at @src/lib/commands/merge.rs:
- Around line 575-601: Update rewrite_tag to detect when an undeclared tag value
matches a fresh ID minted for any input, and emit a specific warning naming that
collision. Preserve the existing behavior of leaving the undeclared tag
unchanged; use the relevant read-group or program ID set based on tag.
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📒 Files selected for processing (6)
crates/fgumi-bam-io/src/header.rscrates/fgumi-sort/src/external.rsdocs/src/guide/migration-from-fgbio.mdsrc/lib/commands/merge.rssrc/lib/commands/zipper.rstests/integration/test_merge_command.rs
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Additional details and impacted files@@ Coverage Diff @@
## main #1050 +/- ##
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… tags When inputs reused an @rg or @pg ID, merge kept the first input's record and dropped the rest, leaving later inputs' reads tagged with an ID that now named another input's read group or program: a read from library libY was labelled libX, and the template-coordinate key ordered it by libX. Nothing warned. That matched `samtools merge -c -p`, not samtools' default, despite the doc comment claiming samtools parity. Records are now compared by content. A record identical to one already written is combined with it, so shards of one sample merge cleanly without samtools' -c/-p. A record whose ID is already used for different content reuses the fresh ID an earlier input's identical record was given, or else is written under the first `{id}.{n}` not declared by any input or already generated, so the IDs are deterministic. The renamed input's @pg PP and @rg PG references are rewritten. A rename changes the translation of any record whose PP names it, so every decision is recomputed from the previous pass until none change, and records are written only after that, never over an earlier input's record; if a PP cycle keeps the decisions from settling, every record whose ID is taken gets a fresh ID. Each rename is logged. The `{id}.{n}` search and the reference rewrite now live in fgumi-bam-io's header module (suffixed_id, with_renamed_reference), shared by merge, zipper and make_unique_program_id. The RG and PG tags of a renamed input's reads are rewritten to the new IDs through a per-record hook, RawExternalSorter::merge_bams_rewriting, which runs before the sort key is extracted so the template-coordinate library follows the rewrite. The hook does no work when no input has a renamed ID. Otherwise a tag naming an ID its input's header does not declare is left unchanged and reported, once per input and tag plus a count, since it could now coincide with a fresh ID. Tests: - header merge: identical records combined; a conflicting @rg renamed; later inputs sharing a conflicting record, or a renamed PP chain, reuse one fresh ID; a third definition gets its own; decisions that never settle fall back to fresh IDs; fresh IDs skip IDs of the same and of later inputs; a @pg rename rewrites PP, cascades through a PP listed before its target, and renames an @rg whose PG named it - end to end, in every merge order: the second input's reads follow `A.1`/`bwa.1`, and an undeclared RG is kept - identical shard headers are written once with tags unchanged - template-coordinate output orders tied templates by the renamed read group's library, for an input's first record and a refilled record
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fgumi merge ignored its command line and wrote no @pg of its own, so a merged BAM carried no record that it had been merged, unlike every other fgumi command and samtools merge. merge now adds one @pg through the shared add_pg_record, after the input headers are merged: ID fgumi (or the first free fgumi.{n} when an input already has one), its version and command line, and PP chained to the last program chain end in merged-header order, which is the last input's when inputs carry separate chains. samtools merge instead adds one @pg per chain end; fgumi keeps to one @pg per command, as #1023 settled. A single input is recorded too. Writing that @pg made merge fail on a command line holding a tab or a non-ASCII character, as every other command already did: the SAM spec limits header values to printable ASCII and noodles refuses to write anything else. build_program_record now passes the command line through header_safe_value, which turns tabs, newlines and carriage returns into spaces (as samtools does for tabs) and escapes any other such character as \u{..}, so a @pg is always writable for every command. Tests pin the @pg for inputs with no programs, a single input, a PP chain, inputs that already carry an fgumi @pg (identical or renamed), and a recorded command line containing a tab; the end-to-end header assertions now include it. header_safe_value has unit tests, and a @pg built from an unprintable command line is written successfully.
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Bug. When merge inputs reused an
@RGor@PGID,fgumi mergekept the first input's record and dropped the rest, but left the later inputs' reads tagged with that ID. Those reads then named another input's read group or program. Repro:in1.bamhas@RG ID:A LB:libXand@PG ID:bwa CL:bwa mem ref1.fa,in2.bamhas@RG ID:A LB:libYand@PG ID:bwa CL:bwa mem ref2.fa, each with one read taggedRG:Z:A PG:Z:bwa. The merged header held onlyA(libX) andbwa(ref1), so in2's read was labelled libX and aligned to ref1, and the template-coordinate key ordered it by libX. Nothing warned. That issamtools merge -c -pbehavior, though the doc comment claimed samtools parity; samtools' default renames the ID and rewrites the read tags.Fix.
@RG/@PGrecords are compared by content:AandA-<random>unless given-c/-p.{id}.{n}not declared by any input. If an earlier input's identical record already got a fresh ID, it reuses that one. The IDs are deterministic, unlike samtools' random suffix.@PG PPand@RG PGreferences are rewritten. A rename changes the translation of any record whosePPnames it, so every decision is recomputed until none change, and records are written only after that, never over an earlier input's record. If aPPcycle keeps the decisions from settling, every record whose ID is taken gets a fresh ID.RG/PGtags of the renamed input's reads are rewritten through a new per-record hook,RawExternalSorter::merge_bams_rewriting, which runs before the sort key is extracted, so the template-coordinate library follows the rename.merge_bamsis unchanged (it calls the new method with a no-op hook).The repro now gives
@RG A (libX),@RG A.1 (libY),@PG bwa (ref1),@PG bwa.1 (ref2), with in2's read taggedRG:Z:A.1 PG:Z:bwa.1.The
{id}.{n}search and the reference rewrite moved intofgumi_bam_io::header(suffixed_id,with_renamed_reference) and are shared by merge, zipper (#1045) andmake_unique_program_id. Thefgumi mergehelp and the fgbio migration guide describe the behavior and how it differs from samtools.fgumi mergestill adds no@PGof its own; that is left for a separate PR.Tests.
test_merge_headers_renames_conflicting_ids(rstest cases): identical records combined; a conflicting@RGrenamed; fresh IDs skip IDs of the same and of later inputs; a@PGrename rewritesPP, cascades through aPPlisted before its target, and renames an@RGwhosePGnames it; later inputs sharing a conflicting record, or a renamedPPchain, reuse one fresh ID; a third definition gets its own.test_merge_records_falls_back_to_fresh_ids_when_decisions_do_not_settle.A.1/bwa.1, and an undeclaredRGis kept. Identical shard headers are written once with tags unchanged. Template-coordinate output orders same-position templates by the renamed read group's library, for an input's first record and for a later record.suffixed_idandwith_renamed_referenceunit tests in fgumi-bam-io.Mutation checks, each confirmed to fail at least one test: no read-tag rewrite; rewriting after key extraction (first-record and refill paths separately); a single conflict pass; renaming identical records; reserving only the first input's IDs; no
PP/PGreference rewrite; no reuse of earlier fresh IDs; deciding conflicts without the cascade.cargo ci-fmt,cargo ci-lintandcargo ci-test(12,276 tests) pass locally.Risk:
fgumi mergeoutput changes in headers, read tags, and template-coordinate ordering; deterministic{id}.{n}renames and integration tests pin the behavior;unsafe: none added, so no CLAUDE.md allowlist update is needed; memory bounds, queue capacity, and thread/backpressure policy: none changed.Fix: Merge combines identical
@RG/@PGrecords and assigns deterministic IDs to conflicting definitions. It rewrites@PG PP,@RG PG, and readRG/PGtags before sort-key extraction. Undeclared tag values remain unchanged and are reported.Shared header helpers now provide ID suffixing and reference rewriting for merge, zipper, and
make_unique_program_id. The update also revises merge help and the fgbio migration guide.fgumi mergedoes not add its own@PGrecord.The author reports that
cargo ci-fmt,cargo ci-lint, andcargo ci-testpassed locally, with 12,276 tests.