JSON metrics: use serde, add --sample-name flag#11
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Addresses NKI-GCF#10. Changes: - Add serde + serde_json; derive Serialize on a new MetricsReport struct whose field names match the existing JSON keys exactly. - Add --sample-name (-s) CLI flag. When provided, SAMPLE_NAME is included in the JSON output; when omitted, the field is absent (backward-compatible). - Fix: the old hand-rolled write_json emitted NaN for FRACTION_DUPLICATION when no reads were processed (0/0). NaN is not valid JSON and would break strict parsers. Now emits null instead. - Drive-by: type-annotate an empty vec in bktree tests to resolve a type-inference ambiguity introduced by serde_json's PartialEq impls. - Add 4 unit tests: serde-vs-legacy value equivalence, sample_name presence/absence, and the zero-reads null-fraction case.
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Hi, I'm Werner. I've got an interest in bioinformatics, especially in cancer genomics, so I figured I'd try to find some connections to the domain through some open-source contributions. I saw your issue #10 and figured I'd send in a PR.
Closes #10.
What this does
write_jsonwith serde (Rust's standard serialization library). The field names and numeric values are unchanged — a unit test parses both the old and new output as JSON and compares them field by field.--sample-name(-s) flag. When provided, aSAMPLE_NAMEfield is included in the JSON output. When omitted, the field is absent, so existing scripts that parse the JSON are unaffected.Things we noticed along the way
FRACTION_DUPLICATIONis 0/0 which the old code wrote asNaN— butNaNis not valid JSON and will break strict parsers. This PR emitsnullinstead. Happy to split it out if you'd prefer a separate fix.Sample output
Without
--sample-name:{"UNPAIRED_READS_EXAMINED":1000,"PAIRED_READS_EXAMINED":5000,...}With
--sample-name my_sample:{"SAMPLE_NAME":"my_sample","UNPAIRED_READS_EXAMINED":1000,...}