feat(merge): add an @PG record for the merge

[nh13]

Stacked on #1050; review that first. This PR's diff is the single commit on top of it.

Change. fgumi merge ignored its command line and wrote no @PG of its own, so a merged BAM carried no record of the merge, unlike every other fgumi command and samtools merge. It 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 (including after fix(merge): rename conflicting @RG/@PG IDs per input and rewrite read tags #1050 renames a conflicting fgumi @PG).
• VN and CL from the fgumi version and the command line.
• PP set 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 fix(header): add one @PG per command instead of one per chain leaf #1023 settled; the code comment and --help say so.
• A single-input merge is recorded too.

For example, merging inputs whose conflicting @PG ID:bwa records #1050 renames gives @PG bwa, @PG bwa.1, @PG fgumi (PP:bwa.1, CL:fgumi merge ...).

Command-line sanitization (all commands). Writing that @PG made merge fail on a command line containing a tab or a non-ASCII character, as every other command already did. The SAM spec (§1.3) limits header values to printable ASCII ([ -~]+), and noodles refuses to write anything else. build_program_record now passes the command line through a new header_safe_value:

• Tabs, newlines and carriage returns become spaces, as samtools does for tabs.
• Any other such character becomes its \u{..} escape, so a non-ASCII path stays legible.

A @PG is now always writable for every command.

Tests.

• test_merge_adds_its_own_program_record (rstest cases): inputs with no programs, a single input, a PP chain, inputs with an identical fgumi @PG (fgumi.1), and inputs whose fgumi @PGs conflict (merge's @PG is fgumi.2, chained to fgumi.1).
• test_merge_program_record_records_command_line: the recorded CL is the command line merge was run with, not a fixed string, and its tab becomes a space. It fails if merge hard-codes "fgumi merge".
• The fix(merge): rename conflicting @RG/@PG IDs per input and rewrite read tags #1050 end-to-end header assertions now include merge's @PG.
• header_safe_value unit tests, and a @PG built from an unprintable command line that writes successfully.

cargo ci-fmt, cargo ci-lint and cargo ci-test (12,287 tests) pass locally.

Risk: Output changes only by adding an @PG header record; deterministic ID selection and chaining to the last program in merged-header order pin it. unsafe: none added or modified; CLAUDE.md allowlist: no update needed. Memory bounds, queue capacity, and thread/backpressure policy: none changed.

fgumi merge now records its version and command line in one @PG record, including for a single input. It chooses fgumi or the next available fgumi.{n} ID. Command-line text is made header-safe: tabs and line breaks become spaces, and other non-printable or non-ASCII characters are escaped.

Tests cover header chaining, ID conflicts, command-line recording, and header-safe values. The author reports that formatting, lint, and test checks passed locally; those results were not independently verified.

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Walkthrough

Merge adds one program record to the output header, chained to the latest input program record. The supplied command line is sanitized before it is stored.

Changes

Merge program record

Layer / File(s)	Summary
Sanitize program-record command lines crates/fgumi-bam-io/src/header.rs	header_safe_value preserves printable ASCII, replaces tabs and line breaks with spaces, and escapes other characters. build_program_record applies this conversion. Tests cover the conversions and writing the sanitized value to a SAM header.
Add a merge program record src/lib/commands/merge.rs, tests/integration/test_merge_command.rs	Merge execution adds one program record using the supplied command line. Tests cover empty and existing program chains, fresh IDs, and command-line recording. Documentation describes the output record and the read-tag behavior when no IDs are renamed.

Priority: ⬇️ Low

Estimated code review effort: 2 (Simple) | ~15 minutes

Change: Feature

Merge Risk: 🔵 Low · up to 858d8

A narrow input case can silently misattribute read provenance metadata.

Pre-merge checks | 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check		The title uses the required Conventional Commit format, names the affected command with the merge scope, and clearly describes the main change. The description is lowercase, imperative, and has no t…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.59%. Comparing base (cf85ceb) to head (858d8cb).

Additional details and impacted files

@@                          Coverage Diff                          @@
##           nh/merge-rename-conflicting-rg-pg    #1051      +/-   ##
=====================================================================
- Coverage                              96.59%   96.59%   -0.01%     
=====================================================================
  Files                                    304      304              
  Lines                                 155974   155993      +19     
=====================================================================
+ Hits                                  150663   150674      +11     
- Misses                                  5311     5319       +8     

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Actionable comments posted: 1

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• 🪄 Fix CodeRabbit comments on this PR

🤖 Prompt to fix review comments

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Inline comments:
Review comments at @src/lib/commands/merge.rs:
- Around line 554-555: Remove the early return from ReadTagRewriter::rewrite
when any_renames is false, so rewrite_tag checks both RG and PG tags even when
no IDs are renamed and can report undeclared tags that might bind to the merge’s
@PG.

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