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fix(counting): distinguish chromosome mismatch from unassigned reads - #176
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…mosome names When mapped reads exist but none lands in a gene, `count_reads` reports "Chromosome name mismatch" without comparing names. These tests fail where the BAM and GTF share a name (directly, or through chromosome_prefix) and keep the mismatch message for disjoint names. All three expect a non-zero exit: whether to abort on this input is a separate question. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
… overlap When mapped reads exist but none is assigned to a gene, check whether any alignment chromosome (after chromosome_prefix / chromosome_mapping) is a GTF chromosome. If one is, report that no reads could be assigned to any gene instead of "Chromosome name mismatch" and its chromosome_mapping advice. The run still fails in both cases; only the diagnostic changes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Avoid claiming no physical overlap when strandedness rejects overlapping reads. Preserve error exits and chromosome-name diagnostics. Add a wrong-strand overlap regression with a successful unstranded control.
Port the separately verified seven-line iterator delta from a9083c, preserving integer addition and channel order.
Apply only the crossbeam-epoch 0.9.20 and libz-sys 1.1.31 version/checksum blocks from b5658a8. These exact pins passed the combined candidate validation.
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When mapped reads cannot be assigned to a gene, RustQC now reports a chromosome-name mismatch only when the effective alignment names and GTF names are disjoint. Shared names produce an assignment diagnostic that directs users to annotation/genome assembly and strandedness settings.
The wording deliberately describes configured gene assignment: a read can physically overlap a gene and still be excluded by
--stranded. The previous version of this PR incorrectly said that no mapped read overlapped a gene in that case. Exit behavior stays nonzero for zero assignment; deciding whether to produce partial/empty outputs is a separate owner decision.Validation of
7c5985on macOS arm64 / Rust 1.90.0:This stays independent of #175's counting work and the #118 → #177 → #178 reader migration. The existing mismatch branch's example chromosome mapping is unchanged. Fresh GitHub CI is reported by the checks on this PR; no full RNA-QC or release acceptance is claimed.
This update is written by GPT-6 on Nico DeVeaux's behalf. The original PR was prepared with Claude Code.