NEWS

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molpathR 0.1.0.9001

• Database construction, merging and persistence share typed table and value contracts. Conflicting primary identities are refused; incomplete links remain explicit. Known legacy empty-table and metadata representations are normalized.
• Actual pathology and XML imports retain patient/sample linkage. VCF integration uses explicit nonreference genotypes and preserves source fields without inventing annotations. Raw FASTQ/BAM data are no longer treated as variant calls.
• Delimited imports use exact field aliases, support semicolon/tab separation, reject malformed outcomes and retain unrecognized source columns.
• VCF ID/INFO/FORMAT/sample values are independent of optional typed backends; BAM fields, FASTQ first-n selection and quality values are repaired. Malformed input and command failures are visible.
• Database writes stage and verify serialization, with recovery on replacement failure. Loading rejects corrupt objects. Upload dispatch preserves the original filename without retaining a deleted temporary path.
• Plot and app filters select the same observations; stale selections are cleared and download formats match their contents. Gene survival groups describe recorded variants, without inferring a negative assay from missing records.
• Small synthetic cohorts work with stable types; generators restore caller RNG and synthetic file dates have an explicit fixed anchor.
• Development citation metadata no longer advertises the unresolving draft DOI; no release or deposit is claimed for this maintenance version.

molpathR 0.1.0

• Standardize the named v5 package logo across README, documentation pages and available application headers, with matching light and dark artwork.

Bug fixes

• mp_query_variants() now correctly filters by classification and variant_type. Previously these arguments were shadowed by the columns of the same name during tidy evaluation, so the filters silently returned every variant.
• mp_read_vcf() now returns an empty result for a header-only VCF instead of a row of NA values, fixing a reversed index range in the text parser.

Features

• Initial release.
• Parsers for VCF, FASTQ, BAM, XML reports, PDF reports, Nexus pathology/clinical exports, and survival data.
• In-memory relational database (molpath_db) with build, merge, validate, save/load operations.
• Query engine with tidy evaluation, variant filtering, free-text search.
• Six visualization functions: variant landscape, mutation spectrum, survival curves, cohort overview, VAF distribution, patient timeline.
• Interactive Shiny application with 6 tabs and cross-tab interactivity.
• Synthetic data generator (mp_example_db()) for demonstration and testing.