Changes in version 1.15.1                        

BUG FIXES

  - Fix igblast() crashing with the cryptic error "argument of length 0"
    when the igblast output contained no AIRR header line. The wrapper
    now returns NULL gracefully and reports the captured igblast/conda
    output so build-time failures are diagnosable. This fixes the
    failing test-igblast.R check on the Bioconductor build machines.
  - Make the "returns a data.frame object" test skip (instead of
    erroring) when the igblast/conda environment is unavailable in the
    test environment.
  - Guard a division-by-zero in igblastwrap.py when zero sequences are
    processed.

                       Changes in version 1.12.1                        

  - fix minor bug that crashed quality_report when some sequences had
    problematic quality and had NA or Inf values
      - this affects summarise_quality and summarise_abi_file

                        Changes in version 1.9.1                        

  - fix igblast cdr3 bug with the contribution of Sebastian Ols
    (@sebbeols)
      - this affects igblast.R function, but mainly the igblast wrapper
        igblastwrap.py

                        Changes in version 1.8.1                        

  - Update citation, scifer is now published in ImmunoInformatics
    (DOI: 10.1016/j.immuno.2024.100046).

                        Changes in version 1.8.0                        

NEW FEATURES

  - New igblast wrapper function to run igblast on fasta sequences
  - igblast function returns the output from a local igblast run with
    any custom database
  - New function requires additional steps for ARM processors, please
    read the README

                 Changes in version 1.7.1 (2024-04-24)                  

BUG FIXES

  - Fix compensation bug due to different compensation matrix positions
    in different .fcs file versions
  - update minor nomenclature to AIRR-standards, column file_ID to
    sequence_id
  - Fix error of HC_individualized_report.Rmd file not being found

NEW FEATURES

  - Update quality thresholds based on a large B cell receptor test
    dataset

scifer 0.99.4 (2022-10-31)

  - Version bump to bioconductor, updated description

scifer 0.99.3 (2022-09-20)

BUG FIXES

  - Fix NOTE when building on windows computer

scifer 0.99.2 (2022-09-08)

NEW FEATURES

  - Update vignette according to Bioconductor
  - Added unit tests for functions

SIGNIFICANT USER-VISIBLE CHANGES

  - Split function fcs_processing() into two functions:
      - fcs_processing()
      - fcs_plot()

BUG FIXES

  - Minor changes to avoid possible bugs

scifer 0.99.1 (2022-08-26)

  - Version bump to fix Bioconductor building error

scifer 0.99.0 (2022-08-10)

  - Adapting package for Bioconductor submission

scifer 0.98.0 (2022-08-09)

  - Major changes in functions
      - nomenclature and all documentation were added following R style
        guidelines
      - Processing flow cytometry data and adding to the
        quality_report() function

scifer 0.1.0 (2022-04-15)

  - Submitted to GitHub

scifer 0.0.1 (2020-08-10)

  - Primordial package created with simple functions and bugs