STAR_2.4.0j

• Fixed a problem with scoring alignments for STARlong. STARlong alignments are slightly modified.
• Fixed a bug introduced in 2.4.0i that dropped a large number of aligmnents for --quantMode TranscriptomeSAM. Transcriptome alignments are now the same as in version 2.4.0h.
• Fixed a problem with lower case read sequences for --outSAMtype BAM options.
• Fixed a bug preventing parameter value to be "-".
• Fixed --genomeLoad LoadAndRemove option.

STAR_2.4.0h

• Added --quantTranscriptomeBAMcompression option.
• Added newline at the end of STAR_VERSION string (contributed by Daniel Nicorici).
• Fixed a bug with parsing the last line of paired FASTA files (contributed by Alex Rolfe).
• Fixed the problem causing Ubuntu error: "sh: 1: Syntax error: Bad fd number".

STAR_2.4.0g1

Note: Mac pre-compiled binary has not been updated in in this release - will update next week.

New Features

• Added --alignSoftClipAtReferenceEnds No option which prevents soft clipping of alignments at the reference (chromosome) ends, for compatibility with Cufflinks/Cuffmerge.
• Added --outSAMflagOR, --outSAMflagAND options to set specific bits of the SAM FLAG.
• --sjdbFileChrStartEnd can now accept multiple files which will be concatenated.
• Added --sysShell option to specify path to bash, in cases where bash is not the default shell.
• --outBAMcompression default changed to 1, which apparently does not change deflation ratio, but is much faster.
• Added --outBAMsortingThreadN option to specify number of threads for BAM sorting. By default (0) it's equal to min(6,runThreadN).

Bug fixes

• Fixed a bug with output score (AS attribute) of some chimeric alignments.
• Fixed wrong output of chimeric junctions boundaries in the Chimeric.out.junction file.
• Fixed the header of the Log.progress.out .
• Fixed a bug that prevented output of transcriptomic alignments (--quantMode TranscriptomeSAM) with 1 base junction overhangs.
• Fixed static and dynamic Linux binaries from 2.4.0g1

STAR_2.4.0g

This release has wrong Linux binaries, please get the 2.4.0g1 release.

STAR_2.4.0f1

• Added read group (RG) BAM attributes to transcriptome BAM (contributed by https://github.com/godotgildor).
• Fixed a bug with double ID field in the RG header line (contributed by https://github.com/godotgildor).
• Fixed a bug in the 2-pass method (--twopass1readsN).
• Fixed a problem with RAM allocation for BAM sorting.

STAR_2.4.0e

• Added manual in PDF.
• New sub-directories: source, bin, doc.
• Output more information about read files into Log.out.
• Fixed some issues that may have caused dropping of multiple reads files.
• Added more thorough error checking for genome generation.
• Fixed a bug causing seg-faults with single-mate alignments for BAM sorting.
• Fixed some compilation issues on Mac OS X. Note that the default Clang lacks openMP support which is required for STAR compilation.
• Added Mac OS X executable.