NEWS

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selexprepR 0.99.6

• Simplify ENA condition messages to address the two new BiocCheck coding practice notes, preserving four-attempt retry and sample-metadata fallback.
• Keep diagnostic accessions, underlying sample failures and retry advice explicit; remove redundant failure wording from the filereport message.

selexprepR 0.99.5

• Align library inference with Python selexprep v0.4.6: retain shared library constants across rounds using per-round offsets, preserve the insert boundary, and avoid ambiguous repeated-core anchors.
• Warn about extraction pools retaining fewer than half their reads or half the best pool's yield, retaining diagnostics in low_yield_rounds. File workflows also retain input_yields and low_yield_inputs per FASTQ, so aggregation cannot mask a poorly matching input.
• Normalize lowercase RNA consistently during detection and primer matching.
• Read ENA BioSample attributes for round inference; handle conflicting and weak PCR-cycle evidence, and stop interpreting ArrayExpress RV sample labels as selection rounds.
• Retry ENA filereport service-error bodies, retain run-level library strategy and sample evidence, and warn when a round pools distinct BioSamples.
• Pin the 240-record catalog and provenance to Python v0.4.6, including the corrected PFOA target class. Add offline Python/R regression references.

selexprepR 0.99.4

• Refuse inferred libraries with a zero-length random region instead of reporting a valid full-insert extraction.
• Rescue well-supported primer cores when noisy outer flanks lower the full-length match rate, without changing the extraction boundary.
• Update the bundled public catalog to the adjudicated Python v0.4.1 snapshot, retaining immutable source and evidence provenance.

selexprepR 0.99.3

• Write LibraryReport and manifest JSON with UTF-8 LF line endings on every platform, preserving deterministic hashes and Python golden-file parity on Windows.

selexprepR 0.99.1

• Initial Bioconductor submission candidate.
• Provides primer inference, extraction, sparse multi-round counting, quality control, reproducibility manifests, FASTQ input, and ENA data discovery.
• Adds selexprep_public_catalog as a documented, reproducibly generated package dataset with immutable snapshot provenance.
• Adds R-native barcode demultiplexing and direct FASTQ/fetch-result input bridges with file hashes retained in the run manifest.