2.5.1a

• Fixed a bug in --quantMode TranscriptomeSAM that prevented output to Aligned.toTranscriptome.out.bam of the reads mapped to the very last annotated transcript.
• Cleaned up the code to remove compilation warnings (thanks to github.com/yhoogstrate).
• Implemented --outSAMunmapped Within KeepPairs option to record unmapped mate adjacent to the mapped one, in case single-end alignments are allowed.
  For multi-mappers, the unmapped mate will be recored mulitple times adjacent to the mappet mate of each alignment.

2.5.0c

• Implemented --genomeSuffixLengthMax option to control max suffix length at the genome generation step.
• Fixed a bug that caused genome generation stalling in some cases.
• In Aligned.toTranscriptome.out.bam (--quantMode TranscriptomeSAM), non-primary SAM flag is assigned to all but one randomly selected alignment in Aligned.toTranscriptome.out.bam .
• Fixed a bug that filtered out some chimeric junctions.
• Fixed a bug that prevented chimeric output for some of the "circular" configurations.

2.5.0b

Bug-fix release:

• Fixed a problem with non-primary alignment flags with --outSAMmultNmax option.
• Added counting of chimeric reads into Log.final.out .
• Fixed a bug in --outSAMfilter KeepOnlyAddedReferences.
• Fixed a minor bug that caused rare seg-faults.
• Fixed a minor bug in STARlong extension at the ends of the read.
• Fixed a seg-fault that occurred when non-default value of --genomeChrBinNbits was used.
• Fixed a seg-fault that occurred when junctions where inserted after inserting reference sequences.

STAR_2.5.0a

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.

STAR_2.4.2a

Major new feature:

• --quantMode GeneCounts option for counting number of reads per gene, similar to htseq-count.

Bug fixes:

• STARlong: fixed --outFilterIntronMotifs and --outSAMstrandField options.
• Yet another fix for --sjdbOverhang logic.
• Error message when shared memory and on the fly junction insertion are used together.
• Fixed a bug causing unnecessary 1 base soft-clipping in rare cases with sparse suffix array.
• Fixed a bug that caused problems with junction motifs in rare cases. Very few alignments affected, <1 per million.

STAR_2.4.1d

• Fixed problems with --sjdbOverhang default and user-defined values.
• Fixed problems with occasional non-adjacent output of multiple alignments into the unsorted BAM file and transcriptome BAM file.
• Fixed a bug causing seg-faults when shared memory options in --genomeLoad are used with --outStd SAM.
• Fixed a bug causing seg-faults for small values of --limitIObufferSize.
• Added STAR long pre-compiled executables.
• Fixed very minor issues with filtering into SJ.out.tab .
• Fixed some bugs in STARlong mapping algorithm.
• Fixed --outFilter BySJout filtering for STARlong.
• Fixed XS attrbutes in STARlong.

2.4.1c

Please use 2.4.1d which contains several bug fixes

• Added latest version of STAR-Fusion as a separate directory.
• Fixed some compilation problems introduced in 2.4.1b.
• Added Mac executable.

2.4.1b

Please use 2.4.1d which contains several bug fixes

• Fixed a bug introduced in 2.4.1a causing serious problems for genomes generated without annotations.
  If you generated a genome without annotations with 2.4.1a please re-generate it.
• Fixed a bug causing seg-faults when generating genomes with a large (>500k) number of junctions.
• Fixed a bug causing seg-faults with --chimOutType WithinBAM for single-end reads.
• Fixed a bug with required --sjdbOverhang at the mapping step.
• STAR-Fusion submodule is included in the STAR_2.4.1b.zip file.

STAR_2.4.1a

Please use 2.4.1d which contains several bug fixes

• The annotations can now be included on the fly at the mapping step, without including them at the genome generation step.
• New option to activate on the fly "per sample" 2-pass method: "--twopassMode Basic".
  2-pass mode can now be used with annotations, which can be included either at the run-time, or at the genome generation step.
• Included link (submodule) to Brian Haas' STAR-Fusion code for detecting fusion transcript from STAR chimeric output: https://github.com/STAR-Fusion/STAR-Fusion
• Included Gery Vessere's shared memory implementation for POSIX and SysV. To compile STAR with POSIX shared memory, use make POSIXSHARED
• New option "--chimOutType WithinBAM" to include chimeric alignments together with normal alignments in the main (sorted or unsorted) BAM file(s).
• New option "--quantTranscriptomeBan Singleend" allows insertions, deletions ans soft-clips in the transcriptomic alignments, which are allowed by some expression quantification software (e.g. eXpress).
• New option "--alignEndsTypeExtension Extend5pOfRead1" to enforce full extension of the 5p of the read1, while all other ends undergo local alignment and may be soft-clipped.

STAR_2.4.0k

Implemented new BAM sorting algorithm that reduces significantly the required RAM.