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STAR_2.5.0a
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@alexdobin alexdobin released this 07 Nov 19:03
· 951 commits to master since this release
STAR_2.5.0a
4e1b232

STAR now uses essential c++11 features and requires gcc 4.7.0 or later.

Major new features:

  • Implemented on the fly insertion of the extra sequences into the genome indexes.
  • Implemented --outSAMmultNmax parameter to limit the number of output alignments for multimappers.
  • Implemented --outMultimapperOrder Random option to output multiple alignments in random order.
    This also randomizes the choice of the primary alignment. Parameter --runRNGseed can be used to set the random generator seed.
    With this option, the ordering of multi-mapping alignments of each read, and the choice of the primary alignment will vary from run to run, unless only one thread is used and the seed is kept constant.

Minor new features:

  • Implemented --outSAMattrIHstart parameter. Setting it to 0 may be required for compatibility with downstream software such as Cufflinks or StringTie.
  • Implemented --outSAMfilter KeepOnlyAddedReferences option.
  • Implemented --help option - thanks to @yhoogstrate for the code.
  • Implemented --alignEndsType Extend3pOfRead1 option for full extension of the 3' end of read 1.
  • Implemented --alignSJstitchMismatchNmax option to allow for mismatches around non-canonical junctions.
  • Implemented --chimSegmentReadGapMax parameter which defines the maximum gap in the read sequence between chimeric segments. By default it is set to 0 to replicate the behavior of the previous STAR versions.
  • Implemented --chimFilter banGenomicN | None options to prohibit or allow the N characters in the vicinity of the chimeric junctions. By default, they are prohibited - the same behavior as in the previous versions.

Bug fixes:

  • For STARlong, increased compilation-time max read length to 500000 and max number of exons to 1000
  • Fixed a bug which caused problems in some cases of genome generation without annotations.
  • Fixed a bug in the --alignEndsType Extend5pOfRead1 option.

Code improvements:

  • Improved compilation flags handling in Makefile - thanks to Christian Krause for the code.
  • Improved treatment of the streams and files - thanks to Alex Finkel for the code.
  • Merged pull request from Nathan S. Watson-Haigh: Makefile for manual;Travis-CI automated build; Update STAR-Fusion submodule to v0.3.1
  • Merged pull request from Alex Finkel to allow 'parameter=value' option formatting, e.g. --runThreadN=8.
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