1.2.1

Rollback to Java 8 for compatibility

1.2.0

Mixcr v3.0 output format support (with -S mixcr)

Now we build with gradle instead of mvn

1.1.10

Add SegmentsToFamilies routine to replace segment IDs by cluster IDs computed using V/J amino acid sequence alignment scores.

1.1.9

• Update the way P-values are computed in CalcDegreeStats to obtain robust results
• Fix the list of amino acid properties (perform proofreading, remove some obsolete ones)
• Use two CDR3 center bounds (-2/+2 and -1/+1) for amino acid property statistics calculation

1.1.8

• Added experimental analysis module CalcDegreeStats that detects clonotypes enriched in neighbors with similar TCR sequence
• Extended the list of CDR3 AA sequence features (Kidera factors, MJ energies)
• Added FilterByFrequency module

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

Feature + fixes

Features:

• Normalized Shannon diversity

Fixes:

• CDR3 AA properties
• Fancy spectratype

Fixes & features

Features

• Add spearman correlation to overlap metrics
• Count number of occurrences / rearrangements when running PoolSamples
• Re-normalize samples on Convert

Fixes

• Switch to milib 1.8, fixing parsing bugs
• Fix plot fancy spectratype

Mixcr 2.1 compatibility patch

See #62

Minor fixes

Fix runner script, optimize immunoseq import