Java 9 compatibility

• Now should work with Java 9

N.B Please ignore An illegal reflective access operation has occurred warnings occurring when running with Java 9, they have no effect on software performance/output whatsoever

Fixes

Fixed Analyze module and --custom-database option.

Post-analysis patch

Improvements

• Remove the --write-binary option. Now all post-analysis and processing is performed on MIGMAP clonotype tables
  • This also allows merging contigs and correcting errors prior to post-analysis
• More efficient implementation of clonotype tree construction under the Analyze routine.

Bug fixes and post analysis routines

Improvements & additions

• Modified API to support clonotype table post-analysis routines
• Basic statistical analysis of somatic hypermutations (Analyze module, see readme)
• Clonotype tree construction (Analyze module, see readme)

Fixes

• Fixed exception with P-segment alignment
• Optimized mutation annotation

Known bugs

• --by-read analysis is not working, use 1.0.1 version or later

Amino acids for hypermutations and helper routines

Improvements

• Added amino acid representation for hypermutations: one-to-one correspondence for nucleotide representation, amino acid sequences are provided on cumulative level, i.e. a single effect is reported for sets of adjacent hypermutations.

Helper routines

• Correct routine - applies a frequency + parsimony-based algorithm that traverses variant tree and appends erroneous variants to their parent clonotypes.
• An option to use custom database and a routine to annotate custom reference file with so-called V/J reference points.

P-segments and optimization

• Added P-segment reporting
• Static compilation to speed up critical parts of code
• Refactoring for some source-code bottlenecks

Some fixes

• Renamed the tool to MiGMAP
• Finally fixed (semingly) all issues with ambiguous IgBlast mappings
• Fixes for --details option
• Add some missing columns to by-read and clonotype table output

Detailed region information

• Added an option (--details) to export nucleotide and amino acid sequences of CDR and FR regions, as well as receptor mRNA contig.
• Fixed some remaining rare bugs related to ambiguous alignment of D segment with IgBlast

Fixes

Major:

• Improved handling of igblast alignments with several top hits. Apparently they resulted in clonotype splitting due to random choice of a single top segment by igblast.
• Fix a bug in FASTA input processing

Minor:

• Time elapsed reporting

Solving complex CDR3 cases

Non-canonical CDR3 workaround

• Fix CDR3 end calculation when J segment reference point is at the boundary or J segment conserved residue is absent with downstream J sequence aligned
• Implement CDR3 start calculation in case V-CDR3 region was not identified by IgBlast
• Add "canonical" CDR3 flag which tells if CDR3 starts with C and ends with F/W
  • Add corresponding filter to output (--allow-noncanonical)