Release Notes

Version 1.3.5: April 14, 2026

CreateGermlines:

CreateGermlines.py now validates the sequence field and raises an informative error if amino acid sequences are detected. Amino acid sequences are not supported; a nucleotide sequence field must be provided.

MakeDb:

MakeDb.py igblast-aa now reports all top-scoring v_call hits in the event of ties. Previously, only the first top-scoring hit was reported. The new behavior aligns with that of the igblast subcommand.

Gene:

Added support for dual-locus TRA/TRD gene detection. getLocus now correctly identifies genes with the TRAV.../DV... naming convention (e.g., TRAV14/DV4) and returns TRA/TRD as the locus.
Fixed a bug where getLocus would raise a TypeError when the gene call was None.

Version 1.3.4: July 31, 2025

MakeDb:

MakeDb.py is now parallelized across input files. The --nproc argument
can be used to restrict the resources used.
Added the flag --partial to MakeDb igblast-aa to pass incomplete alignment results. As igblastp (as at igblast 1.22.0) only uses the V germline database, all sequences will be missing the junction and j_call fields and be considered incomplete. Specifying --partial will allow these sequences to be processed ignoring the missing fields.

Documentation:

Added a “Contributing” section to the documentation menu for community guidelines.
Updated “Contact”.

Version 1.3.3: May 14, 2025

Updated dependencies to address deprecation warnings. Replaced pkg_resources with packaging and importlib.
Bumped minimum Python version to 3.10.0 and updated requirements to: numpy>=1.23.2, scipy>=1.9.3, pandas>=1.5.0, biopython>=1.81, PyYAML>=6.0, setuptools>=65.5.0, presto>=0.7.1, airr>=1.3.1, packaging>=21.3, importlib-resources>=6.4.0.

Version 1.3.1: March 27, 2025

Active development has moved from Bitbucket to GitHub (https://github.com/immcantation/changeo).
Documentation updates.
Various updates to internals to avoid deprecation warnings.
Updates in requirements: Python 3.7.0, biopython>=1.81 and packaging>=23.2.

Version 1.3.0: December 11, 2022

Various updates to internals and error messages.

AssignGenes:

Added support for .fastq files. If a .fastq file is input, then a corresponding .fasta file will be created in output directory.
Added support for C region alignment calls provide by IgBLAST v1.18+.

MakeDb:

Added support for C region alignment calls provide by IgBLAST v1.18+.

Version 1.2.0: October 29, 2021

Updated dependencies to presto >= v0.7.0.

AssignGenes:

Fixed reporting of IgBLAST output counts when specifying --format airr.

BuildTrees:

Added support for specifying fixed omega and hotness parameters at the commandline.

CreateGermlines:

Will now use the first allele in the reference database when duplicate allele names are provided. Only appears to affect mouse BCR light chains and TCR alleles in the IMGT database when the same allele name differs by strain.

MakeDb:

Added support for changes in how IMGT/HighV-QUEST v1.8.4 handles special characters in sequence identifiers.
Fixed the imgt subcommand incorrectly allowing execution without specifying the IMGT/HighV-QUEST output file at the commandline.

ParseDb:

Added reporting of output file sizes to the console log of the split subcommand.

Version 1.1.0: June 21, 2021

Fixed gene parsing for IMGT temporary designation nomenclature.
Updated dependencies to biopython >= v1.77, airr >= v1.3.1, PyYAML>=5.1.

MakeDb:

Added the --imgt-id-len argument to accommodate changes introduced in how IMGT/HighV-QUEST truncates sequence identifiers as of v1.8.3 (May 7, 2021). The header lines in the fasta files are now truncated to 49 characters. In IMGT/HighV-QUEST versions older than v1.8.3, they were truncated to 50 characters. --imgt-id-len default value is 49. Users should specify --imgt-id-len 50 to analyze IMGT results generated with IMGT/HighV-QUEST versions older than v1.8.3.
Added the --infer-junction argument to MakeDb igblast, to enable the inference of the junction sequence when not reported by IgBLAST. Should be used with data from IgBLAST v1.6.0 or older; before igblast added the IMGT-CDR3 inference.

Version 1.0.2: January 18, 2021

AlignRecords:

Fixed a bug caused the program to exit when encountering missing sequence data. It will now fail the row or group with missing data and continue.

MakeDb:

Added support for IgBLAST v1.17.0.

ParseDb:

Added a relevant error message when an input field is missing from the data.

Version 1.0.1: October 13, 2020

Updated to support Biopython v1.78.
Increased the biopython dependency to v1.71.
Increased the presto dependency to 0.6.2.

Version 1.0.0: May 6, 2020

The default output in all tools is now the AIRR Rearrangement standard (--format airr). Support for the legacy Change-O data standard is still provided through the --format changeo argument to the tools.
License changed to AGPL-3.

AssignGenes:

Added the igblast-aa subcommand to run igblastp on amino acid input.

BuildTrees:

Adjusted RECORDS to indicate all sequences in input file. INITIAL_FILTER now shows sequence count after initial min_seq filtering.
Added option to skip codon masking: --nmask.
Mask :, ,, ), and ( in IDs and metadata with -.
Can obtain germline from GERMLINE_IMGT if GERMLINE_IMGT_D_MASK not specified.
Can reconstruct intermediate sequences with IgPhyML using --asr.

ConvertDb:

Fixed a bug in the airr subcommand that caused the junction_length field to be deleted from the output.
Fixed a bug in the genbank subcommand that caused the junction CDS to be missing from the ASN output.

CreateGermlines:

Added the --cf argument to allow specification of the clone field.

MakeDb:

Added the igblast-aa subcommand to parse the output of igblastp.
Changed the log entry FUNCTIONAL to PRODUCTIVE and removed the IMGT_PASS log entry in favor of an informative ERROR entry when sequences fail the junction region validation.
Add –regions argument to the igblast and igblast-aa subcommands to allow specification of the IMGT CDR/FWR region boundaries. Currently, the supported specifications are default (human, mouse) and rhesus-igl.

Version 0.4.6: July 19, 2019

BuildTrees:

Added capability of running IgPhyML on outputted data (--igphyml) and support for passing IgPhyML arguments through BuildTrees.
Added the --clean argument to force deletion of all intermediate files after IgPhyML execution.
Added the --format argument to allow specification input and output of either the Change-O standard (changeo) or AIRR Rearrangement standard (airr).

CreateGermlines:

Fixed a bug causing incorrect reporting of the germline format in the console log.

ConvertDb:

Removed requirement for the NP1_LENGTH and NP2_LENGTH fields from the genbank subcommand.

DefineClones:

Fixed a biopython warning arising when applying --model aa to junction sequences that are not a multiple of three. The junction will now be padded with an appropriate number of Ns (usually resulting in a translation to X).

MakeDb:

Added the --10x argument to all subcommands to support merging of Cell Ranger annotation data, such as UMI count and C-region assignment, with the output of the supported alignment tools.
Added inference of the receptor locus from the alignment data to all subcommands, which is output in the LOCUS field.
Combined the extended field arguments of all subcommands (--scores, --regions, --cdr3, and --junction) into a single --extended argument.
Removed parsing of old IgBLAST v1.5 CDR3 fields (CDR3_IGBLAST, CDR3_IGBLAST_AA).

Version 0.4.5: January 9, 2019

Slightly changed version number display in commandline help.

BuildTrees:

Fixed a bug that caused malformed lineages.tsv output file.

CreateGermlines:

Fixed a bug in the CreateGermlines log output causing incorrect missing D gene or J gene error messages.

DefineClones:

Fixed a bug that caused a missing junction column to cluster sequences together.

MakeDb:

Fixed a bug that caused failed germline reconstructions to be recorded as None, rather than an empty string, in the GERMLINE_IMGT column.

Version 0.4.4: October 27, 2018

Fixed a bug causing the values of _start fields to be off by one from the v1.2 AIRR Schema requirement when specifying --format airr.

Version 0.4.3: October 19, 2018

Updated airr library requirement to v1.2.1 to fix empty V(D)J start coordinate values when specifying --format airr to tools.
Changed pRESTO dependency to v0.5.10.

BuildTrees:

New tool.
Converts tab-delimited database files into input for IgPhyML

CreateGermlines:

Now verifies that all files/folder passed to the -r argument exist.

Version 0.4.2: September 6, 2018

Updated support for the AIRR Rearrangement schema to v1.2 and added the associated airr library dependency.

AssignGenes:

New tool.
Provides a simple IgBLAST wrapper as the igblast subcommand.

ConvertDb:

The genbank subcommand will perform a check for some of the required columns in the input file and exit if they are not found.
Changed the behavior of the -y argument in the genbank subcommand. This argument is now featured to sample features only, but allows for the inclusion of any BioSample attribute.

CreateGermlines:

Will now perform a naive verification that the reference sequences provided to the -r argument are IMGT-gapped. A warning will be issued to standard error if the reference sequence fail the check.
Will perform a check for some of the required columns in the input file and exit if they are not found.

MakeDb:

Changed the output of SEQUENCE_VDJ from the igblast subcommand to retain insertions in the query sequence rather than delete them as is done in the SEQUENCE_IMGT field.
Will now perform a naive verification that the reference sequences provided to the -r argument are IMGT-gapped. A warning will be issued to standard error if the reference sequence fail the check.

Version 0.4.1: July 16, 2018

Fixed installation incompatibility with pip 10.
Fixed duplicate newline issue on Windows.
All tools will no longer create empty pass or fail files if there are no records meeting the appropriate criteria for output.
Most tools now allow explicit specification of the output file name via the optional -o argument.
Added support for the AIRR standard TSV via the --format airr argument to all relevant tools.
Replaced V, D and J BTOP columns with CIGAR columns in data standard.
Numerous API changes and internal structural changes to commandline tools.

AlignRecords:

Fixed a bug arising when space characters are present in the sequence identifiers.

ConvertDb:

New tool.
Includes the airr and changeo subcommand to convert between AIRR and Change-O formatted TSV files.
The genbank subcommand creates MiAIRR compliant files for submission to GenBank/TLS.
Contains the baseline and fasta subcommands previously in ParseDb.

CreateGermlines

Changed character used to pad clonal consensus sequences from . to N.
Changed tie resolution in clonal consensus from random V/J gene to alphabetical by sequence identifier.
Added --df and -jf arguments for specifying D and J fields, respectively.
Add initial sorting step with specifying --cloned so that clonally ordered input is no longer required.

DefineClones:

Removed the chen2010 and ademokun2011 and made the previous bygroup subcommand the default behavior.
Renamed the --f argument to --gf for consistency with other tools.
Added the arguments --vf and -jf to allow specification of V and J call fields, respectively.

MakeDb:

Renamed --noparse argument to --asis-id.
Added asis-calls argument to igblast subcommand to allow use with non-standard gene names.
Added the GERMLINE_IMGT column to the default output.
Changed junction inference in igblast subcommand to use IgBLAST’s CDR3 assignment for IgBLAST versions greater than or equal to 1.7.0.
Added a verification that the SEQUENCE_IMGT and JUNCTION fields are in agreement for records to pass.
Changed behavior of the igblast subcommand’s translation of the junction sequence to truncate junction that are not multiples of 3, rather than pad to a multiple of 3 (removes trailing X character).
The igblast subcommand will now fail records missing the required optional fields subject seq, query seq and BTOP, rather than abort.
Fixed bug causing parsing of IgBLAST <= 1.4 output to fail.

ParseDb:

Added the merge subcommand which will combine TSV files.
All field arguments are now case sensitive to provide support for both the Change-O and AIRR data standards.

Version 0.3.12: February 16, 2018

MakeDb:

Fixed a bug wherein specifying multiple simultaneous inputs would cause duplication of parsed pRESTO fields to appear in the second and higher output files.

Version 0.3.11: February 6, 2018

MakeDb:

Fixed junction inferrence for igblast subcommand when J region is truncated.

Version 0.3.10: February 6, 2018

Fixed incorrect progress bars resulting from files containing empty lines.

DefineClones:

Fixed several bugs in the chen2010 and ademokun2011 methods that caused them to either fail or incorrectly cluster all sequences into a single clone.
Added informative message for out of memory error in chen2010 and ademokun2011 methods.

Version 0.3.9: October 17, 2017

DefineClones:

Fixed a bug causing DefineClones to fail when all are sequences removed from a group due to missing characters.

Version 0.3.8: October 5, 2017

AlignRecords:

Ressurrected AlignRecords which performs multiple alignment of sequence fields.
Added new subcommands across (multiple aligns within columns), within (multiple aligns columns within each row), and block (multiple aligns across both columns and rows).

CreateGermlines:

Fixed a bug causing CreateGermlines to incorrectly fail records when using the argument --vf V_CALL_GENOTYPED.

DefineClones:

Added the --maxmiss argument to the bygroup subcommand of DefineClones which set exclusion criteria for junction sequence with ambiguous and missing characters. By default, bygroup will now fail all sequences with any missing characters in the junction (--maxmiss 0).

Version 0.3.7: June 30, 2017

MakeDb:

Fixed an incompatibility with IgBLAST v1.7.0.

CreateGermlines:

Fixed an error that occurs when using the --cloned with an input file containing duplicate values in SEQUENCE_ID that caused some records to be discarded.

Version 0.3.6: June 13, 2017

Fixed an overflow error on Windows that caused tools to fatally exit.
All tools will now print detailed help if no arguments are provided.

Version 0.3.5: May 12, 2017

Fixed a bug wherein .tsv was not being recognized as a valid extension.

MakeDb:

Added the --cdr3 argument to the igblast subcommand to extract the CDR3 nucleotide and amino acid sequence defined by IgBLAST.
Updated the IMGT/HighV-QUEST parser to handle recent column name changes.
Fixed a bug in the igblast parser wherein some sequence identifiers were not being processed correctly.

DefineClones:

Changed the way X characters are handled in the amino acid Hamming distance model to count as a match against any character.

Version 0.3.4: February 14, 2017

License changed to Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0).

CreateGermlines:

Added GERMLINE_V_CALL, GERMLINE_D_CALL and GERMLINE_J_CALL columns to the output when the -cloned argument is specified. These columns contain the consensus annotations when clonal groups contain ambiguous gene assignments.
Fixed the error message for an invalid repo (-r) argument.

DefineClones:

Deprecated m1n and hs1f distance models, renamed them to m1n_compat and hs1f_compat, and replaced them with hh_s1f and replaced mk_rs1nf, respectively.
Renamed the hs5f distance model to hh_s5f.
Added the mouse specific distance model mk_rs5nf from Cui et al, 2016.

MakeDb:

Added compatibility for IgBLAST v1.6.
Added the flag --partial which tells MakeDb to pass incomplete alignment results specified.
Added missing console log entries for the ihmm subcommand.
IMGT/HighV-QUEST, IgBLAST and iHMMune-Align parsers have been cleaned up, better documented and moved into the iterable classes changeo.Parsers.IMGTReader, change.Parsers.IgBLASTReader, and change.Parsers.IHMMuneReader, respectively.
Corrected behavior of D_FRAME annotation from the --junction argument to the imgt subcommand such that it now reports no value when no value is reported by IMGT, rather than reporting the reading frame as 0 in these cases.
Fixed parsing of IN_FRAME, STOP, D_SEQ_START and D_SEQ_LENGTH fields from iHMMune-Align output.
Removed extraneous score fields from each parser.
Fixed the error message for an invalid repo (-r) argument.

Version 0.3.3: August 8, 2016

Increased csv.field_size_limit in changeo.IO, ParseDb and DefineClones to be able to handle files with larger number of UMIs in one field.

Renamed the fields N1_LENGTH to NP1_LENGTH and N2_LENGTH to NP2_LENGTH.

CreateGermlines:

Added differentiation of the N and P regions the the REGION log field if the N/P region info is present in the input file (eg, from the --junction argument to MakeDb-imgt). If the additional N/P region columns are not present, then both N and P regions will be denoted by N, as in previous versions.
Added the option ‘regions’ to the -g argument to create add the GERMLINE_REGIONS field to the output which represents the germline positions as V, D, J, N and P characters. This is equivalent to the REGION log entry.

DefineClones:

Improved peformance significantly of the --act set grouping method in the bygroup subcommand.

MakeDb:

Fixed a bug producing D_SEQ_START and J_SEQ_START relative to SEQUENCE_VDJ when they should be relative to SEQUENCE_INPUT.
Added the argument --junction to the imgt subcommand to parse additional junction information fields, including N/P region lengths and the D-segment reading frame. This provides the following additional output fields: D_FRAME, N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH.
The fields N1_LENGTH and N2_LENGTH have been renamed to accommodate adding additional output from IMGT under the --junction flag. The new names are NP1_LENGTH and NP2_LENGTH.
Fixed a bug that caused the IN_FRAME, MUTATED_INVARIANT and STOP field to be be parsed incorrectly from IMGT data.
Ouput from iHMMuneAlign can now be parsed via the ihmm subcommand. Note, there is insufficient information returned by iHMMuneAlign to reliably reconstruct germline sequences from the output using CreateGermlines.

ParseDb:

Renamed the clip subcommand to baseline.

Version 0.3.2: March 8, 2016

Fixed a bug with installation on Windows due to old file paths lingering in changeo.egg-info/SOURCES.txt.

Updated license from CC BY-NC-SA 3.0 to CC BY-NC-SA 4.0.

CreateGermlines:

Fixed a bug producing incorrect values in the SEQUENCE field on the log file.

MakeDb:

Updated igblast subcommand to correctly parse records with indels. Now igblast must be run with the argument outfmt "7 std qseq sseq btop".
Changed the names of the FWR and CDR output columns added with --regions to <region>_IMGT.
Added V_BTOP and J_BTOP output when the --scores flag is specified to the igblast subcommand.

Version 0.3.1: December 18, 2015

MakeDb:

Fixed bug wherein the imgt subcommand was not properly recognizing an extracted folder as input to the -i argument.

Version 0.3.0: December 4, 2015

Conversion to a proper Python package which uses pip and setuptools for installation.

The package now requires Python 3.4. Python 2.7 is not longer supported.

The required dependency versions have been bumped to numpy 1.9, scipy 0.14, pandas 0.16 and biopython 1.65.

DbCore:

Divided DbCore functionality into the separate modules: Defaults, Distance, IO, Multiprocessing and Receptor.

IgCore:

Remove IgCore in favor of dependency on pRESTO >= 0.5.0.

AnalyzeAa:

This tool was removed. This functionality has been migrated to the alakazam R package.

DefineClones:

Added --sf flag to specify sequence field to be used to calculate distance between sequences.
Fixed bug in wherein sequences with missing data in grouping columns were being assigned into a single group and clustered. Sequences with missing grouping variables will now be failed.
Fixed bug where sequences with “None” junctions were grouped together.

GapRecords:

This tool was removed in favor of adding IMGT gapping support to igblast subcommand of MakeDb.

MakeDb:

Updated IgBLAST parser to create an IMGT gapped sequence and infer the junction region as defined by IMGT.
Added the --regions flag which adds extra columns containing FWR and CDR regions as defined by IMGT.
Added support to imgt subcommand for the new IMGT/HighV-QUEST compression scheme (.txz files).

Version 0.2.5: August 25, 2015

CreateGermlines:

Removed default ‘-r’ repository and added informative error messages when invalid germline repositories are provided.
Updated ‘-r’ flag to take list of folders and/or fasta files with germlines.

Version 0.2.4: August 19, 2015

MakeDb:

Fixed a bug wherein N1 and N2 region indexing was off by one nucleotide for the igblast subcommand (leading to incorrect SEQUENCE_VDJ values).

ParseDb:

Fixed a bug wherein specifying the -f argument to the index subcommand would cause an error.

Version 0.2.3: July 22, 2015

DefineClones:

Fixed a typo in the default normalization setting of the bygroup subcommand, which was being interpreted as ‘none’ rather than ‘len’.
Changed the ‘hs5f’ model of the bygroup subcommand to be centered -log10 of the targeting probability.
Added the --sym argument to the bygroup subcommand which determines how asymmetric distances are handled.

Version 0.2.2: July 8, 2015

CreateGermlines:

Germline creation now works for IgBLAST output parsed with MakeDb. The argument --sf SEQUENCE_VDJ must be provided to generate germlines from IgBLAST output. The same reference database used for the IgBLAST alignment must be specified with the -r flag.
Fixed a bug with determination of N1 and N2 region positions.

MakeDb:

Combined the -z and -f flags of the imgt subcommand into a single flag, -i, which autodetects the input type.
Added requirement that IgBLAST input be generated using the -outfmt "7 std qseq" argument to igblastn.
Modified SEQUENCE_VDJ output from IgBLAST parser to include gaps inserted during alignment.
Added correction for IgBLAST alignments where V/D, D/J or V/J segments are assigned overlapping positions.
Corrected N1_LENGTH and N2_LENGTH calculation from IgBLAST output.
Added the --scores flag which adds extra columns containing alignment scores from IMGT and IgBLAST output.

Version 0.2.1: June 18, 2015

DefineClones:

Removed mouse 3-mer model, ‘m3n’.

Version 0.2.0: June 17, 2015

Initial public prerelease.

Output files were added to the usage documentation of all scripts.

General code cleanup.

DbCore:

Updated loading of database files to convert column names to uppercase.

AnalyzeAa:

Fixed a bug where junctions less than one codon long would lead to a division by zero error.
Added --failed flag to create database with records that fail analysis.
Added --sf flag to specify sequence field to be analyzed.

CreateGermlines:

Fixed a bug where germline sequences could not be created for light chains.

DefineClones:

Added a human 1-mer model, ‘hs1f’, which uses the substitution rates from from Yaari et al, 2013.
Changed default model to ‘hs1f’ and default normalization to length for bygroup subcommand.
Added --link argument which allows for specification of single, complete, or average linkage during clonal clustering (default single).

GapRecords:

Fixed a bug wherein non-standard sequence fields could not be aligned.

MakeDb:

Fixed bug where the allele ‘TRGVA*01’ was not recognized as a valid allele.

ParseDb:

Added rename subcommand to ParseDb which renames fields.

Version 0.2.0.beta-2015-05-31: May 31, 2015

Minor changes to a few output file names and log field entries.

ParseDb:

Added index subcommand to ParseDb which adds a numeric index field.

Version 0.2.0.beta-2015-05-05: May 05, 2015

Prerelease for review.