add input_reads and output_reads in report.json for single-cell-pna denoise and single-cell-pna sample-calling

[ptajvar]

input_reads and output_reads are typically reported for all steps of the PNA pipeline but they were missing in denoise and sample calling.

Fixes: PNA-2715

Type of change

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce it when relevant.

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• If a new tool or package is included, I have updated dependencies in pyproject.toml and cited it properly
• I have checked my code and documentation and corrected any misspellings
• I have documented any significant changes to the code in CHANGELOG.md

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Note

Low Risk
Read-count reporting only in JSON reports and tests; no changes to denoising or sample-calling algorithms or data paths.

Overview
Adds input_reads and output_reads to report.json for single-cell-pna denoise and single-cell-pna sample-calling, matching other PNA pipeline stages.

For denoise, counts come from summing reads_in_component on the input PXL and on the written output (when denoising is off, both values are equal). For sample-calling, each per-sample report compares reads attributed to that sample’s components in the pool input vs the dehashed output; the pooled sample_calling_total report uses full-pool input reads and sums output reads excluding the undetermined sample.

Report models, CLI wiring, create_final_report, and tests are updated accordingly; CHANGELOG documents the addition.

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