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fix(zipper): rename a conflicting unmapped @PG instead of dropping it - #1045
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ChangesZipper Program Records
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~25 minutes Change: Bug fix Sequence Diagram(s)sequenceDiagram
participant ChainBuilder
participant ZipperMergeConfig
participant ZipperMergeStep
ChainBuilder->>ChainBuilder: Derive program-ID renames from paired BAM headers
ChainBuilder->>ZipperMergeConfig: Pass rename map
ZipperMergeConfig->>ZipperMergeStep: Configure PG rewrite lookup
ZipperMergeStep->>ZipperMergeStep: Rewrite copied unmapped-read PG values
Merge Risk: ⚪ Minimal · up to Conflicting unmapped Pre-merge checks |
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## main #1045 +/- ##
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Coverage 96.59% 96.59%
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Files 304 304
Lines 155379 155704 +325
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- 🪄 Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @src/lib/commands/zipper.rs:
- Around line 381-382: Update both @PG ordering descriptions associated with
merge_program_records to clarify that unmapped-only records come first, while
identical shared records are emitted once in mapped order. Preserve the existing
descriptions of zipper’s added @PG and fgbio ZipperBams behavior.
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Actionable comments posted: 1
- 🪄 Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @src/lib/commands/zipper.rs:
- Around line 803-819: Update encode_unmapped_template_records to receive the PG
rename map and rewrite Z-typed PG tags using the same mapping as merge_raw_with,
including when exclude_missing_reads is false. Add coverage for an unmapped-only
read on both execution paths to verify renamed PG values.
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Builds on #1023. When both inputs held an @pg with the same ID but different content, zipper dropped the unmapped copy. Any unmapped program whose PP named that ID then pointed at the unrelated mapped record, and zipper's own @pg could chain to the unmapped side instead of the aligner (e.g. unmapped `samtools import` vs mapped `samtools view`). Both records are now kept. The unmapped copy gets a fresh `{id}.{n}` ID not used in either header (the scheme make_unique_program_id uses), and every PP in the unmapped records that named it is rewritten. A rename can make a record that matched its mapped namesake differ from it, so conflicts are recomputed until none remain. Identical records are still written once, in the mapped position, and unmapped records still come first. fgbio ZipperBams fails on this input instead (htsjdk's addProgramRecord rejects the duplicate ID); the code comment and the fgbio migration guide record the difference. A read-level PG tag from an unmapped read is rewritten through the same renames, so the read keeps naming the program that produced it rather than its mapped namesake. This covers tags copied onto merged reads and unmapped-only reads written without a merge, on both the serial path and the pipeline chain (--threads >= 4). The copy rule is unchanged: the unmapped PG is copied only when the mapped read has none. The unmapped-only encoder now takes the tag lookups instead of the header it ignored, so ZipperMergeConfig drops its unused output_header field. Tests, each at threads 1 and 4, compare exact (ID, PN, PP) triples and full records against expected @pgs written out field by field: - two PP-linked chains whose mapped leaf is not last in header order, so zipper's PP must follow the PP links (fgbio passes the inputs through verbatim, ZipperBamsTest.scala:137) - the extract -> align -> zipper flow adds `fgumi.1` - a same-ID conflict renames the unmapped copy and rewrites its PP - an identical shared record is written once - the fresh ID skips IDs used in either header - a rename cascades through a PP that named the renamed ID - a read PG naming a renamed ID follows the rename on merged and unmapped-only reads (including a cascaded rename); unrenamed and unknown IDs, a mapped read's own PG, and a read without PG are unchanged
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Title: fix(zipper): rename a conflicting unmapped @pg instead of dropping it
Base:
main(#1023 has merged)Builds on #1023 (merged), which fixes the duplicate @pg (one @pg per command, chained to the last leaf, unmapped @pg records merged before mapped ones).
Bug. When both inputs hold an @pg with the same ID but different content, zipper on #1023 drops the unmapped copy. Any unmapped program whose PP named that ID then points at the unrelated mapped record, and zipper's own @pg can chain to the unmapped side instead of the aligner. Repro: unmapped
samtools (import) | fgumi (correct, PP:samtools), mappedbwa-mem3 | samtools (view, PP:bwa-mem3). The output wasfgumi (PP:samtools) | bwa-mem3 | samtools (view) | fgumi.1 (PP:fgumi), sofgumi correctnow claims to followsamtools viewand zipper chains tofgumi correct.Fix. Both records are kept. The unmapped copy gets a fresh
{id}.{n}ID that isn't used in either header (the same scheme asmake_unique_program_id), and every PP in the unmapped records that named it is rewritten. A rename can make a record that matched its mapped namesake differ from it, so conflicts are recomputed until nothing changes. Identical records are still written once, in the mapped position, and unmapped records still come first. The repro now givessamtools.1 (import) | fgumi (correct, PP:samtools.1) | bwa-mem3 | samtools (view) | fgumi.1 (zipper, PP:samtools).Read
PGtags. A record'sPG:Ztag names an@PGID as text, so after a rename an unmapped read taggedPG:Z:samtoolswould point at the mappedsamtools view. zipper now rewrites an unmapped read'sPGtag through the same renames (PG:Z:samtoolsbecomesPG:Z:samtools.1), both when it copies the tag onto a merged read and when it writes an unmapped-only read without a merge. Both the serial path and the pipeline chain (--threads >= 4) do this. The unmapped-only encoder now takes the tag lookups instead of the header it ignored, soZipperMergeConfigdrops its unusedoutput_headerfield. The copy rule is unchanged: the unmappedPGis copied only when the mapped read has none, as in fgbio'scopyTags, and a mapped read's ownPGis never changed. With no conflicting ID the rename map is empty and the per-tag check is skipped.fgbio
ZipperBamsfails on this input instead: it drops an unmapped @pg only when an equal mapped record exists (ZipperBams.scala:95), and htsjdk'sSAMFileHeader.addProgramRecordthrows on the duplicate ID. The code comment and a new "Program Records (@pg)" section in the fgbio migration guide record the difference, including the readPGrewrite.Tests (each at
--threads 1and--threads 4, exact(ID, PN, PP)triples in order plus full-record equality, with fgumi's expected record written out field by field rather than built by the helper under test):chains_zipper_pg_to_aligner: two PP-linked chains whose mapped leaf (SortSam) is not the last @pg in header order, so zipper's PP must follow the PP links. The input programs pass through verbatim, as fgbio asserts inZipperBamsTest.scala:137. fgbio adds no @pg of its own, so the single fgumi @pg is fgumi behavior.after_fgumi_extract: the unmapped header already hasID:fgumi, so zipper addsfgumi.1chained to the aligner.renames_conflicting_unmapped_pg: the repro above.dedups_identical_shared_pg: an identical shared record is written once, in the mapped position.rename_skips_existing_ids:samtools.1is taken in the mapped header andsamtools.2in the unmapped one, so the rename issamtools.3and the PP naming it is rewritten.rename_cascades_through_pp: an unmappedfgumi (PP:samtools)textually equals its mapped namesake but differs oncesamtoolsis renamed, so it becomesfgumi.1. It is listed beforesamtools, so a single pass would miss it.read_pg_tag_follows_renamed_unmapped_pg(rstest cases, with one merged and one unmapped-only pair): a readPGnaming the renamed ID follows it on both; an unrenamed ID, an unknown ID, a mapped read's ownPG(including one naming the shared ID), and noPGare unchanged. Every output record of both pairs is checked.read_pg_tag_follows_cascaded_rename: a readPGnaming an ID renamed only on a later pass is rewritten too, on merged and unmapped-only reads.Disabling the merge-time read-tag rewrite on the serial path fails only the
threads_1read-tag cases, and disabling it on the chain path fails only thethreads_4ones. Disabling the unmapped-only rewrite fails the renamed, cascaded, and mapped-PG-wins cases at both thread counts. Each path is pinned.Mutation checks, each run against the header tests: chaining to the last @pg in header order, merging mapped first, dropping the unique-ID suffix, dropping renamed records, skipping the PP rewrite, treating identical records as conflicts, reserving only mapped IDs, a single pass, and comparing records before the PP rewrite. Each mutation fails at least one test. The only survivor, which skips recording each fresh ID as used, is equivalent:
{id}.{n}splits back uniquely at its last dot, so two conflicting IDs never get the same fresh ID.zipper --helpsays nothing about @pg, so the help text is unchanged.Risk:
zipperheader and readPGoutput changes; tests pin the renamed IDs, references, ordering, and tags. Nounsafechange; theCLAUDE.mdallowlist is unchanged. No memory-bound, queue-capacity, or thread/backpressure change.Retain conflicting unmapped
@PGrecords under fresh IDs, and rewrite theirPPreferences and copied readPGtags. Deduplicate identical records.The PR description reports header and read-tag tests for serial and pipeline paths, plus mutation checks. Test execution results were not provided.