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NEWS.md

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chiimp dev

  • Switched from YAML-based to CSV-based configuration system, now using R options() (#98, #99)
  • Added support for imperfect primer matches, IUPAC ambiguity codes in primers, and read modification actions based on matched primers (#97)

chiimp 0.4.1

  • Overhauled unit tests with more modular saved inputs and expected outputs (#92)
  • Made warnings encountered in the chiimp script display as they occur, rather than at the end (#91)
  • Made load_dataset warn about repeated Sample+Replicate+Locus entries across rows (#90)
  • Made load_config warn about any unrecognized configuration file entries (#88)

chiimp 0.4.0

  • Fixed desktop icon drag-and-drop for recent Linux distributions (#85)
  • Fixed genotype summary table row ordering for certain edge cases (#81)
  • Fixed pandoc error with newer RStudio versions (>= 2022.02) by finding pandoc automatically (#75)
  • Made load_csv use custom row names if given (#74)
  • Made installer obey site-wide R configuration if present (#72)
  • Fixed superfluous quotes in report HTML file when rendered with newer pandoc (#69)
  • Fixed spurious warnings during histogram plotting due to missing data (#66)
  • Added option for custom text in genotype summary tables for untested locus/sample combinations (#64)
  • Made save_csv automatically create any parent directories as needed (#63)
  • Fixed handling of extra pheatmap arguments in plot_dist_mat (#62)

chiimp 0.3.1

  • Fixed icon setup on Mac OS (#56).

chiimp 0.3.0

  • Improved icon setup on Mac OS (#48).
  • Added support for use of reverse primers in locus-matching (#47).
  • Made read count ratio thresholds for PCR stutter and artifact sequence flagging customizable (#46).
  • Added drag-and-drop usage message when desktop icon is opened directly (#44).
  • Added load_csv and save_csv functions to centralize loading and saving tabular data (#43).
  • Reorganized installer and wrapper scripts (#38).
  • Added support for demo scripts and integration testing in Mac OS (#32).

chiimp 0.2.3

  • Fixed package checks and testing on latest R development releases (#27).
  • Fixed test behavior on Windows and improved test organization (#16).
  • Added documentation corrections and improvements.

chiimp 0.2.2

  • Fixed heatmap plotting via updated plot_heatmap for cases with blank results and only one unique non-blank value (#22).
  • Added check in analyze_dataset for locus name mismatches between dataset table and locus attributes table (#21).
  • Added check in prepare_dataset for missing data directory (#20).
  • Added check in prepare_dataset for zero-detected-files case.
  • Added check in load_dataset for missing data files.
  • Added check in full_analysis to warn if any input data files are completely empty.

chiimp 0.2.1

  • Minor improvements to release process (#14).
  • Fixed install script for Mac OS (#13).
  • Fixed file-saving on Windows (#12).
  • Fixed installation on Windows for usernames with spaces (#11).
  • Added automatic categorization of genotyping results for samples from known individuals (#8).
    • Added function to pair samples with known correct genotypes, match_known_genotypes.
    • Added function to categorize results of genotyping for known individuals, categorize_genotype_results.
    • Enabled categorization features in summarize_dataset when Name column is supplied in results summary data frame.

chiimp 0.2.0

  • Restructured code to avoid analyzing multiplexed samples more than once (#3).
  • Reorganized output into per-sequence-file (full) and per-sample (filtered) sections (#5).
    • Added a new saving function, save_seqfile_data, to save a directory tree of per-sequence-file output files starting from the first shared directory in the input file paths.
    • Moved functionality from analyze_sample into a new analyze_seqs function to be used as a separate step (enabling shared processing between multiplexed samples in a single data file for #3).
    • Split data list from analyze_dataset output into two separate lists called files and samples.
  • Added sequence name matching to analyze_dataset. The summary data frame now has Allele1Name and Allele2Name columns, and the sample data frames a SeqName column, matching any sequence recognized as a called allele from any sample in the current analysis (or a previous analysis if the allele table is provided).
  • Improved histogram function to recognize more categories of unique sequences including sequences called as alleles elsewhere, and return the counts-by-length data by category in a list.
    • Removed histogram2 to centralize functionality in histogram.
  • Fixed bugs causing failure of report generation for completely blank dataset analysis results (#7).
  • Removed summarize_sample_by_length function.
  • Clarified behavior of summarize_sample functions to allow any combination of TRUE/FALSE values in the Ambiguous/Stutter/Artifact entries. Previously only the first (highest-count) case would be flagged.
  • Added features to track and filter ambiguous sequences (#4).
    • Added column named Ambiguous to analyze_sample output to flag sequences with non-ACTG characters.
    • Added entry named Ambiguous to summarize_sample output to track filtering of sequences with non-ACTG characters.

chiimp 0.1.0

  • Initial release