explaincommand to show help text for common concepts (starting with the sample metadata CSV used bydemuxandtrim) (#89)trimnow supports custom forward and/or reverse adapter sequences (#88)trimnow supports passing additional command-line arguments through to cutadapt (#87)
trimnow 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)
treenow supports defining seq set groupings via positions in an alignment (#81)treenow supports writing FigTree settings in NEXUS output files (#79)treenow writes seq set groupings in NEXUS output files (#67)
treedefaults to simpler color-coding logic for sets of sequences (for sequences in multiple sets, by default the last set's color is used) (#77)igblasthas its version pinned at 1.21.0 rather than left unspecified (#70)
igblastnow handles crashes during file input more clearly (#75)phixcan accept a custom path for the read counts CSV file (#74)
convertnow handles edge cases for sequence input and tabular output by always including a sequence description column in the output (#63)
msawill now bypass calling MUSCLE when called with just a single input sequence, avoiding a crash (#62)convertwill now obey a custom sequence description column name if one is given with--col-seq-desc(#60)getreadscommand is now compatible with the latest available version of bcl2fastq, v2.20.0.422 (#58)treecommand can now handle assigning a color code when exactly one sequence set is defined (#57)
summarizecommand will automatically use all available references for a given species if a species is given but no references (#50)treecommand for creating and formatting phylogenetic trees (#44)- support for additional arguments for
getreadscommand passed through to bcl2fastq (#43) msacommand for building multiple sequence alignments with MUSCLE (#41)
convertcommand and underlying input/output features now handles sequence descriptions (#51)identitycommand now uses a custom sequence ID column if one is given (#49)
- Automatic usage of all available references for a given species in
igblastcommand (#39) identitycommand for calculating pairwise identity between arbitrary queries and references (#31, #37)- Support for showing basic tree topology for Newick-format files in
showcommand (#33)
- Uppercase file extensions are now supported by the
showcommand (#35) - broken pipes (such as from
igseq something | something else) are now handled gracefully (#30)
- Support for .afa (as FASTA) and .fq (as FASTQ) in input/output handling (#26)
- 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)
- vdj-match now skips references that are missing gene segments but were only included implicitly rather than directly named (#25)
- 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)
- Show a warning for zero file matches in list and show commands (#8)
- 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)
First beta release