Qmarcou IGoR Versions Save

1.4.0 (April 11, 2020)

A brief description of the release content's

New features:

• Add feature extracting CDR3s based on alignments (by @alfaceor)
• New IGL and IGK models for humans (by @alfaceor)

Bug fixes:

• fix out of bound access for Dinucleotide markov model internal probabilities (by @Thopic)

Miscellaneous :

• New script igor-compute_pgen to calculate pgen for a single sequence (by @alfaceor)
• Add error messages for unknown supplied chain or output subargument (by @qmarcou)
• Add new option -getdatadir to output the path of default models directory (by @alfaceor)

New features:

• Add ---best_gene_only boolean for alignments
• Allow for template specific alignment offsets
• Allow for reversed offsets use via command line
• Pygor package installable via pip (by @penuts7644)
• New documentation website available at: https://qmarcou.github.io/IGoR/

Bug fixes:

• Fix autogen creation of man and html README
• Fix semi colon separated files for gene anchors (human BCR, mice TRB)
• Fix pygor package broken imports and functions (by @penuts7644)
• Fix IGoR directory creation and installation problems (by @smoe)
• Fix bug on number of scenarios for the scenario counter CL
• Fix alignment threshold for --ntCDR3 sequences

Miscellaneous :

• Split documentation in several files.
• Create a proper manpage.
• Improve error handling for alignment issues (report faulty genomic template)
• Improve error handling for some input files reading
• make the autogen.sh and build_release scripts executable (by @NickEngland)
• Clean and make the Pygor package PEP8 compliant (by @penuts7644)

New features:

• Enable CDR3 sequences alignment using defined gene anchors via --ntCDR3
• better quality random seed generation
• show a progress bar for alignment, inference/evaluation and generation.
• add independent Nmer hypermutation models in the repository
• add mouse beta chain model

Bug fixes:

• replace the use of default_random_engine by a 64bits mersenne twister

Miscellaneous :

• make a proper licensing under GNU-GPLv3
• create a ChangeLog for better traceability
• clean some Eclipse config file from the repo
• remove events initialization message duplication
• transition to asciidoc documentation
• add juman BCR CDR3 anchors

First release hosted on the new official GitHub repository Previous releases were hosted at https://bitbucket.org/qmarcou/igor/downloads/