Minor update

• Add more details to report (sample name, command line arguments)
• Improve pipeline verbosity, fix ambiguous messages
• Fix incorrect parent region for boundary deletion cases
• --unmapped unmapped.fastq option will store unmapped reads to separate file

Improvements and fixes

Updates

• Improved CLI, several fixes
• Analysis report generation with --report
• Quality/non-coding/... filter now applies to per-read data also
• V/D/J CDR3 markup (V end, etc) and V/D/J truncation are now reported
• Changed quality handling: filtering each read based on min quality, not clonotypes based on min average quality
• Flags for non-coding, incomplete, etc clonotypes

Bug fixes

• J reference point boundary case fix
• Mutation sub-region assignment fix

Remastered

• Optimized parallelization
• Better reference file support: can specify multiple genes
• By-read and piped output
  • Storing read headers
• Better mutation reporting
  • Added indels
  • Reporting mutations in D/J germline
  • Mutations split by FR/CDR
• More intelligent quality filtering, only N regions and mutations

Minor allele support

• Added support for minor alleles, i.e. ones other than *01
• A pair important anti-crash fixes
• Fixed clonotype frequency counting

Fixes for binaries and more

• Added correct path to win igblast executable
• Re-packed binaries to add missing references
• Fixed a bug preventing some igblast14 references from loading

New species and IgBlast 1.4 support

v0.4

Data bundle cleanup

Functional release (testing)

Re-implemented clonotype reporting. Quality calculation fix

Basic functionality

Several major fixes. Added mutation reporting and clone level detalization

First release

IgBlast output parsing, IgBlast parallelization, clonotype assembly, quality filtering