MiXCR v2.1.10

• Chain distribution is back in report file
• V/J chimera detection and elimination mechanism; new parameter minChimeraDetectionScore both alignments in R1 and R2 should be greater than this value
• Smarter second fine alignment step, new parameter alignmentBoundaryTolerance, now this mechanism is triggered even if alignment boundary not perfectly matches read boundary in the opposite mate-pair; minor bug fixes
• Fixed NPE in VDJCHit#getIdentity. Commands like mixcr exportClones ... -cBestIdentityPercent ... were affected
• New align action report line added No target with both V and J alignments; fix for inaccurate value for Alignment failed because of low total score
• Enable asserts for non-release builds, increases chance of detecting subtile error conditions, by trading-off some performance; has no effect on release builds

MiXCR v2.1.9

• Built-in library upgrade to v1.5, many fixes, new species Nannospalax galili (see library release notes for complete list of changes)
• Fix wrong number of chimeric alignments in report with --write-all option
• Removed wrong -v in text warnings in align action
• Added -OmergerParameters.identityType= parameter on align stage (possible values are Unweighted and MinimalQualityWeighted), default value is Unweighted. MinimalQualityWeighted can be used for more reliable merging of paired-end data with low quality ends
• Dropped out-of-the-box support for files produced with repseq.io libraries v1.0 and 1.1

MiXCR v2.1.8

• Fixes possible IOException during report output on Lustre file system

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v2.1.7

• Fixes bug leading to IOException if report file not exists. (#295)

MiXCR v2.1.6

Major changes

• (beta) Added JSON-formatted reports. Use --json-report option in align, extendAlignments, assemblePartial or assemble actions to create JSON report or append it to already existing report file (jsonl). This feature is intended to simplify batch analysis, and analysis automation. E.g. jq util can be used to aggregate information from multi-json-report files.
• Report file appends are made atomic. Now you can safely specify the same report file name in several invocations of MiXCR, even if you run several instances of MiXCR in parallel. Should also work for NFS and other remote FS, suppporting file locking.
• Added chains column in export (-chains and -topChains)

Minor changes

• Several new counters added to align report
• Added proper filtering for alleles with wildcard symbols in featureToAlign region
• Fixed bug in align report (wrong total count in rare cases) #265
• Documentation added for filterAlignments

MiXCR v2.1.5

• Fixed backward compatibility of *.vdjca files produced by MiXCR 2.1.2 and lower with kaligner2.

MiXCR v2.1.4

• RepSeq.IO updated to 1.2.9, default built-in library updated to 1.4 (read library changelog here and here).

MiXCR v2.1.3

• Minimal thresholds added for V and J alignments in extendAlignments
• minimalNOverlap in assemblePartial changed to 7
• Information on k-mer diversity added to alignPartial report file
• Fix: MiXCR now correctly detects *.fa files as FASTA formatted
• Details of V/J Extension during extendAlignments are now added to target description, and can be retrieved using -targetDescriptions field in exportAlignments

MiXCR v2.1.2

• Fixed rare IllegalArgumentException in extendAlignments action
• Fixed rare NPE in align action
• Added sortAlignments utility action

MiXCR v2.1.1

⚠️ -defaultAnchorPoints fields have changed. Values for array elements with indices 11, 12, 15, 16 moved to 10, 13, 14, 17 respectively, compared to 2.1; 11, 12, 15, 16 now represents the same as was in 2.0 branch

⚠️ -p default_affine on assemble stage not needed any more, all parameters on this stage are inferred automatically from input *.vdjca file

Changes linked to RNA-Seq / WGS repertoire extraction feature

• Additional check for the same V hits in merging sequences in assemblePartial
• Fix: list of C hits limited by relativeMinScore in assemblePartial
• Not aligned mates from fully aligned opposite PE reads are now taken into assemblePartial procedure (case when V and J parts of the target read are shorter than 12 nt)
• Additional consistency cehcks in assemblePartial, overlaps of non-CDR3-covering mates of PE reads are also taken into account
• -p option in assemblePartial enabled by default; deprecated; will be removed in 2.2
• Added -d option in assemblePartial to drop non-assembled partial reads for reduction of output file size
• More sophisticated algorithm for alignment-guided merging of paired-end reads in align

Other major changes

• Several anchor point positions in export points changed their meaning (see warning above for details).
• Fixed absent space in AA. Seq. ... column name and excessive space in the end of several column names (affects exportClones and exportAlignments with -v option; fixes compatibility with VDJTools v1.1.3 and below).
• Fixes NPE in exportClones in some cases with mmu reference
• Added sortAlignments action. Sort *.vdjca files by read id, allows diffing alignments after assembleParial and other actions that shuffle records inside file.
• Fixed incorrect behaviour of exportClones and exportAlignments in cases like mixcr exportAlignments -p full -descrR1 ...

Minor changes

• Multiple reads in exportAlignmentsPretty and filterAlignments should be now specified as -i 123 -i 456 or -i 123,456 etc.
• --reads-ids in exportAlignmentsPretty and --readsIds in filterAlignments both renamed to --read-ids
• infrastructure for post-build tests in Travis CI