Version 0.7.0

Added

• explain command to show help text for common concepts (starting with the sample metadata CSV used by demux and trim) (#89)
• trim now supports custom forward and/or reverse adapter sequences (#88)
• trim now supports passing additional command-line arguments through to cutadapt (#87)

Changed

• trim now allows the species to be left unspecified and/or the Type column in the samples CSV to be missing or blank, in which case any applicable adapter sequences will be used in the cutadapt commands (#85)

Fixed

• identity now handles an optional alternate sequence ID column correctly for the reference input file (#95)
• igblast no longer hangs with empty input (#94)
• vdj-gather can handle multiple input paths with sequences for the same segment (for example, IGHV sequences from two germline references) (#93)

Version 0.6.0

Added

• tree now supports defining seq set groupings via positions in an alignment (#81)
• tree now supports writing FigTree settings in NEXUS output files (#79)
• tree now writes seq set groupings in NEXUS output files (#67)

Changed

• tree defaults to simpler color-coding logic for sets of sequences (for sequences in multiple sets, by default the last set's color is used) (#77)
• igblast has its version pinned at 1.21.0 rather than left unspecified (#70)

Fixed

• igblast now handles crashes during file input more clearly (#75)
• phix can accept a custom path for the read counts CSV file (#74)

Version 0.5.1

Changed

• convert now handles edge cases for sequence input and tabular output by always including a sequence description column in the output (#63)

Fixed

• msa will now bypass calling MUSCLE when called with just a single input sequence, avoiding a crash (#62)
• convert will now obey a custom sequence description column name if one is given with --col-seq-desc (#60)
• getreads command is now compatible with the latest available version of bcl2fastq, v2.20.0.422 (#58)
• tree command can now handle assigning a color code when exactly one sequence set is defined (#57)

Version 0.5.0

0.5.0 - 2023-01-04

Added

• summarize command will automatically use all available references for a given species if a species is given but no references (#50)
• tree command for creating and formatting phylogenetic trees (#44)
• support for additional arguments for getreads command passed through to bcl2fastq (#43)
• msa command for building multiple sequence alignments with MUSCLE (#41)

Fixed

• convert command and underlying input/output features now handles sequence descriptions (#51)
• identity command now uses a custom sequence ID column if one is given (#49)

Version 0.4.0

Added

• Automatic usage of all available references for a given species in igblast command (#39)
• identity command for calculating pairwise identity between arbitrary queries and references (#31, #37)
• Support for showing basic tree topology for Newick-format files in show command (#33)

Fixed

• Uppercase file extensions are now supported by the show command (#35)
• broken pipes (such as from igseq something | something else) are now handled gracefully (#30)

Version 0.3.0

Added

• Support for .afa (as FASTA) and .fq (as FASTQ) in input/output handling (#26)

Changed

• Replaced Rhesus germline reference "bernat2021" with "kimdb" version 1.1, containing additions and corrections since the original publication, and added a CSV of germline reference information (#28)

Fixed

• vdj-match now skips references that are missing gene segments but were only included implicitly rather than directly named (#25)

Version 0.2.0

Added

• Human germline FASTAs from IMGT (#21)
• support for FASTA/FASTQ/CSV/TSV query inputs for the igblast and related
  commands (#18, #19)
• convert command for FASTA/FASTQ/CSV/TSV file conversion, in place of the
  more limited tab2seq command (#14, #16)
• Rhesus germline HV and HJ allele FASTAs from
  10.4049/jimmunol.1800342 (#13)

Version 0.1.1

Changed

• Show a warning for zero file matches in list and show commands (#8)

Fixed

• IgBLAST output is now shown even if it crashes (#12)
• Header-only CSV/TSV files no longer crash the show command (#8)
• summarize command now works with multiple references (#7)
• vdj-match and summarize commands now work as intended via igblast, and all
  have basic automated tests (#5)
• igblastn arguments can now be given with a two-dash prefix to ensure they
  aren't interpreted as igseq arguments (#4)
• Duplicate FASTA paths found in vdj-gather will no longer result in
  duplicated output sequences (#2)

Version 0.1.0

First beta release