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Adds BamRecordCodecBenchmark, a JMH benchmark of BAM record decoding and encoding; there was none.
Synthetic records held in memory as uncompressed BAM, so inflation and I/O are left out: 200,000 paired 150 bp reads with typical aligner tags (SHORT) and 2,000 15 kb reads (LONG).
decode (fixed fields only), decodeEverything, and decodeFromBgzf, which reads through a BlockCompressedInputStream as a BAM file is read.
encode*: decode, do one thing to each record, encode again. Untouched, a flag change, a tag set, an absent tag removed, every field decoded; plus encodeFromMemory for records built in memory. A decoded record writes its stored bytes unchanged until something marks them stale, and these show what each kind of change costs.
Two PRs that follow are measured with it: keeping the stored bytes when an absent tag is removed, and reading the fixed fields in one call.
Summary by CodeRabbit
Chores
Added performance benchmarks for BAM record decoding and encoding, covering compressed and uncompressed data, different read sizes, and record changes.
These benchmarks provide performance measurements for common record-processing scenarios. No end-user behavior changes are included.
There was no benchmark of BAM record coding. This one decodes, or
decodes and re-encodes, synthetic records held in memory as
uncompressed BAM, so that inflation and I/O are left out: paired 150 bp
reads with typical aligner tags, and 15 kb long reads. One variant
decodes through a BlockCompressedInputStream instead, as a BAM file is
read, to show what a change to decoding is worth with inflation counted.
The encode benchmarks differ only in what is done to each decoded
record before it is encoded again: nothing, a flag change, a tag set,
an absent tag removed, or every field decoded. A decoded record writes
its variable-length bytes unchanged until something marks them stale,
and these show what each kind of change costs.
Adds a JMH benchmark that generates synthetic BAM records and measures decoding and encoding across short and long read shapes. The benchmark covers uncompressed and BGZF input, field access, record modifications, and encoding records built in memory.
Changes: BAM codec benchmark
Layer / File(s)
Summary
Synthetic records and BAM inputs src/benches/java/htsjdk/samtools/BamRecordCodecBenchmark.java
Defines short and long read shapes, generates synthetic records with configured tags, and prepares uncompressed and BGZF-compressed BAM input.
Measures uncompressed and BGZF decoding. A separate benchmark accesses record names, CIGARs, bases, qualities, and attributes.
Record encoding cases src/benches/java/htsjdk/samtools/BamRecordCodecBenchmark.java
Measures encoding untouched records and records after selected changes or eager field decoding. Also measures encoding prebuilt in-memory records. Uses a counting output stream to count encoded bytes.
The targeted benchmark command needs correction, but the benchmark remains runnable with a corrected selector.
Pre-merge checks: 4 · 1
Failed checks: 1 warning
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Docstring Coverage
Docstring coverage is 37.50% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documenta…
Write docstrings for the functions missing them to satisfy the coverage threshold.
Passed checks: 4 passed
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Title check
The title "Add a JMH benchmark of BAMRecordCodec" names the primary change: a new JMH benchmark class for BAM record decoding and encoding. The raw summary confirms that BamRecordCodecBenchmark is the…
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Full details: Title check
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The title "Add a JMH benchmark of BAMRecordCodec" names the primary change: a new JMH benchmark class for BAM record decoding and encoding. The raw summary confirms that BamRecordCodecBenchmark is the only file added (+283 lines), and the PR objectives describe the same benchmark. The title is short, specific, and free of file lists or vague wording. One minor gap: it does not name the SHORT/LONG input shapes or the BGZF input path, but the title does not need to cover every detail.
Full details: Docstring Coverage
Explanation
Docstring coverage is 37.50% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 8 functions across 1 files.
Resolution
Write docstrings for the functions missing them to satisfy the coverage threshold.
Finishing Touches: 💡 1
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Actionable comments posted: 1
🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at
@src/benches/java/htsjdk/samtools/BamRecordCodecBenchmark.java:
- Around line 37-38: Update the targeted JMH invocation in the
BamRecordCodecBenchmark class documentation to use the generated benchmark name,
BamRecordCodecBenchmark.decode, so the example selects the decode benchmark.
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Adds
BamRecordCodecBenchmark, a JMH benchmark of BAM record decoding and encoding; there was none.SHORT) and 2,000 15 kb reads (LONG).decode(fixed fields only),decodeEverything, anddecodeFromBgzf, which reads through aBlockCompressedInputStreamas a BAM file is read.encode*: decode, do one thing to each record, encode again. Untouched, a flag change, a tag set, an absent tag removed, every field decoded; plusencodeFromMemoryfor records built in memory. A decoded record writes its stored bytes unchanged until something marks them stale, and these show what each kind of change costs.Two PRs that follow are measured with it: keeping the stored bytes when an absent tag is removed, and reading the fixed fields in one call.
Summary by CodeRabbit