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MiXCR v2.1.1
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@dbolotin dbolotin released this 02 Mar 22:04
· 3340 commits to develop since this release
v2.1.1
c36bbcc

⚠️ -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
Assets 3
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