Mar 7, 2023
Release 1.21.0
*Added gaps to *_alignment_aa fields (such as sequence_alignment_aa) to reflect gaps in nucleotide sequence alignment.

*Added the new AIRR format field: sequence_aa.  This is direct translation (no gaps) of nucleotide sequence using the reading frame determined by nucleotide sequence alignment to its closet germline V gene.

*Added the new AIRR format field: d_frame.  This is the D gene frame that is in-frame with the J gene coding frame.  IgBLAST offers built-in IGHD gene frame support for mouse as defined by Ichihara Y et al (European Journal of Immunology Volume 19, Issue 10 p. 1849-1854).  Users can use their own custom D gene definition with IgBLAST according to their needs.
	
	
Oct 24, 2022
Release 1.20.0
*Added capability to use custom V gene FWR/CDR annotation 

Jun 02, 2022
Release 1.19.0
*Added logic to handle the case where there is a unrearranged J gene downstream of the VDJ rearrangement. 
	
Dec 13, 2021
Release 1.18.0

*Added capability to report C genes for Ig sequences.
	

Feb 26, 2021
Release 1.17.1

*Fixed annotation errors for TCR J genes.


Oct 16, 2020
Release 1.17.0

*Added the V frame shift field to indicate if there is an internal frame shift in V gene translation frame (for example, nucleotide deletions/insertions found in pseudogenes or caused by somatic mutations).

*The definition for whether a sequence is productive or not has now been updated.  Previously, a sequence is considered to be productive if the V(D)J rearrangement frame is in-frame and no stop codon is found.  Now the definition for a productive sequence includes no internal frame shift in V gene, in addition to previous requirement of V(D)J rearrangement frame being in-frame and no stop codon.
	
	
Apr 10, 2020
Release 1.16.0

*Added ability to use custom organism.  

*Added ability to extend J gene alignment at 3' end.

*Added the AIRR complete_vdj field.

*Deleted parameters that are used for standard BLAST but not for IgBLAST.


Jan 21, 2020
Release 1.15.0
*Added support for the FWR4 annotation.

*The previous "-penalty" parameter was renamed as V_penalty to be consistent with other IgBLAST penalty options

*Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters

*Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

Apr 29, 2019
Release 1.14.0
*Making AIRR format more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending "reversed" to seqid when query is in reversed orientation, using standard locus names such as IGH, TRB instead of traditional VH, VB etc.

*Loosening criteria to show CDR3 end by allowing the first FWR4 base to be missing.	

*Bug fix: Restoring seqid for no result case in AIRR rearrangement format.  Printing IgBlast version number instead of Blast version number with -version option.
	
Mar 7, 2019
Release 1.13.0
*Determine the V gene reading frame from the end of FWR3 region instead of end of V gene.  This is to allow proper determination of the frames for rearrangements that have insertions or deletions near the V gene end.

*Increase allowed distance between V gene end and J gene start to 225 bp to allow detection of ultra long D/N region.

*Package the edit_imgt_file.pl script, the internal_data and optional_files folders into the IgBlast release such that it is easy for user to install.
	
Nov 26, 2018
*Release 1.12.0
*Increase allowed distance between V gene end and J gene start positions (from 90 bp to 150 bp) as well as between V gene end and D gene start positions (from 55 to 120 bp) to accommodate extremely long VDJ junctions found in some antibodies. 

Oct 25, 2018
*Release 1.11.0
*Change the 0-based coordinate system to 1-based coordinate system in AIRR format (with -outfmt 19 parameter) for sequence start positions per the new AIRR Rearrangement Schema ( http://docs.airr-community.org/en/latest/datarep/rearrangements.html ).

Aug 24, 2018
*Release 1.10.0
*Fix some processes not exiting under cpu full load condition

April 30, 2018
*Release 1.9.0
*Adding the AIRR rearrangement tabular format	

Sept 22, 2017
*Release 1.8.0
*Re-engineered multi-threading mechanism which significantly shortens the processing time. Default to use 4 threads.

*Added ability to accept the SRA accession directly as query input.

*Lower the default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and from -3 to -2, respectively). This is to better accommodate moderately mutated sequences. 	

April 19, 2017
*Release 1.7.0
*Make nucleotide overlaps at VDJ junctions an option (-allow_vdj_overlap) and default is set to no overlap allowed.  Previous versions were hard-coded to allow nucleotide overlaps at VDJ junctions.
*Use alignment length instead of percent identity as tiebreaker for hits with identical blast scores.
*Allow custom J gene mismatch penalty.
*Add CDR3 start and stop to sub-region table
	
Oct 26, 2016
* Release 1.6.1
* Added clonotype report
* Enabled multi-threading option -num_threads
	
April 25, 2016
* Release 1.5.0
* Added CDR3 annotation 
* Added option for extending at 5' side
* Default to IMGT region (was Kabat previously)
	
July 17, 2014
* Release 1.4.0
* Added capability to analyze monkey sequences.

February 19, 2014
* Release 1.3.0
* Better handling of non-Ig sequences
* Include makeblastdb binary with pre-compiled releases

September 5, 2013
* Release 1.2.0
* Add capability for T cell receptor analysis.

December 12, 2012
* Release 1.1.0
* Added option to specify minimal required D gene matches.
* Result summary now reports if there is stop codon and if the rearrangement is productive or not.
* Improved D and J gene match logic.
* Added capability to analyze rat and rabbit sequences.

March 20, 2012
* First stand alone release
