STAR 2.4.2a 2015/06/19
Implemented --quantMode GeneCounts option for counting number of reads per gene, similar to htseq-count.
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 2015/05/19
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.
Added --runDirPerm option for permissions of run-time directories.


STAR 2.4.1c 2015/04/24
Added latest version of STAR-Fusion as a separate directory.
Fixed some compilation problems introduced in 2.4.1b.
Added Mac executable.


STAR 2.4.1b 2015/04/23
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 2.4.1a 2015/04/17
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.

2.4.0k 03/30/2015
Implemented new BAM sorting algorithm that reduces significantly the required RAM.

2.4.0j 02/04/2015
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.

2.4.0i 01/14/2015
Fixed a bug with the _STARtmp temporary directory name for the 2-pass runs.
Fixed a bug causing seg-faults for genome generation.
Fixed a bug causing seg-faults for --quantMode TranscriptomeSAM

2.4.0h 12/09/2014
Fixed the problem causing Ubuntu error: "sh: 1: Syntax error: Bad fd number".
Added --quantTranscriptomeBAMcompression option.
Add 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).

2.4.0g 11/26/2014
Fixed a bug with output score (AS attribute) of some chimeric alignments.
Added --alignSoftClipAtReferenceEnds No option which prevents soft clipping of alignments at the reference (chromosome) ends, for compatibility with Cufflinks/Cuffmerge.
Fixed wrong output of chimeric junctions boundaries in the Chimeric.out.junction file.
Added --outSAMflagOR, --outSAMflagAND options to set specific bits of the SAM FLAG.
--sjdbFileChrStartEnd can now accept multiple files which will be concatenated.
Fixed the header of the Log.progress.out .
Fixed a bug that prevented output of transcriptomic alignments (--quantMode TranscriptomeSAM)  with 1 base junction overhangs.
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).

2.4.0f1 10/30/2014
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.

2.4.0e 10/24/2014
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.

2.4.0d 09/25/2014
Added .gitignore.
Fixed the problem with 2nd field in the read name shorter than 3 bases (non-Illumina fastq).
Added --outBAMcompression option.
Added --bamRemoveDuplicatesType and --bamRemoveDuplicatesMate2basesN options.
Added --outWigType wiggle read1_5p read2 options.
Added --outWigNorm option.

2.4.0c 09/07/2014
Automated git version.
Fixed a problem with overflowing SJ buffer.
Implemented options --twopass1readsN, --twopassSJlimit, --readMapNumber.

2.4.0b 08/29/2014
Fixed problems with spaces in --outFilePrefixName.
Fixed version information.

2.4.0a 08/11/2014
Implemented --outFilterMismatchNoverReadLmax option for a more consistent control of mismatches.

2.3.1z16 08/05/2014
Implemented --outWigReferencesPrefix option to filter references in the signal output.
Implemented --runMode inputAlignmentsFromBAM --inputBAMfile

2.3.1z15  
Implemented --outWigType bedGraph read1_5p option.
Fixed a problem with chimeric alignments with overlapping segments.
Fixed a problem with processing of fasta read input.

2.3.1z14 07/24/2014
Implemented 0x200 SAM flag for reads that did not pass Illumina filtering (i.e. contain “Y” as the 3rd character in the second field of the read name)
Implemented comma-separated lists in the --outSAMattrRGline read groups that will assign different read groups to multiple comma-separated read files in --readFilesIn

2.3.1z13 07/04/2014
Fixed problems with STARlong.

2.3.1z12 06/30/2014
Fixed problems with SAM/BAM output to stdout.

2.3.1z11 06/27/2014
Switched to htslib samtools library.
Fixed problem with indel near known splice junctions.
Fixed problem with FASTA reads input.

2.3.1z10 06/20/2014
Fixed problem with compilation, samtools/ZLIB related.

2.3.1z9 06/19/2014
2.3.1z8 
2.3.1z7 
Fixed problems with transcriptomic output.
Changed --sjdbFileChrStartEnd importing to allow direct import from SJ.out.tab

2.3.1z6 05/30/2014
2.3.1z5 05/30/2014
Fixed a bug causing problems with multiple zipped input files.
Preliminary release of BAM sorting and wiggle output

2.3.1z4 05/06/2014
Preliminary release with transcriptome output.

2.3.1z2 04/29/2014
Fixed a bug causing problems in some chimeric alignments.
Fixed a bug causing overflowing of SAM ISIZE.
Fixed chimeric output problems with --outFilterType BySJout option
Added extra Log.out messages for multi-threaded jobs.

2.3.1z1 03/13/2014
SAM header changes: 
    removed "cl:" attribute from the @PG line, output it as a separate comment line
    added --outSAMheaderHD, --outSAMheaderPG, --outSAMheaderCommentFile options
Added --outTmpDir, which set the path forSTAr temporary directory independent of --outFileNamePrefix

2.3.1z 02/05/2014
Fixed the incorrect behavior of --genomeLoad LoadAndRemove option.

2.3.1y 01/24/2014
Added read group sam attribute via --outSAMattrRGline parameter.
Fixed gcc 4.7.0. compilation problem.
Correct reverse complementarity of all IUPAC nucleotide codes in the SAM output.

2.3.1x 01/08/2014
Fixed a bug with --alignEndsType EndToEnd.

2.3.1v 12/21/2013
Added --alignEndsType EndToEnd option to align reads end-to-end, i.e. prohibit soft-clipping.
--outSAMattributes now allows to specify the SAM attributes in the desired combination and order.
Implemented standard (samtools-like) NM and MD tags.
Added --outSAMmapqUnique parameter (=255 by default), MAPQ value for unique mappers.

2.3.1u 11/23/2013
Added --outSAMreadID={Standard,Number} parameter to output read numbered read IDs.
Aded --outSAMmode NoQS option to suppress output of quality scores.

2.3.1t 11/20/2013
Fixed a bug that prevented alignment to the very beginning of the first reference.

2.3.1s 11/06/2013
Fixed a bug that produced incorrect placement of short deletions.

2.3.1r 10/01/2013
Compilation option to output "local alignment chanins".
Compilation option to output suffix array as a text file.

2.3.1q 08/15/2013
Fixed a problem with junction overhang in SJ.out.tab file for overlapping mates.

2.3.1p 04/13/2013
Fixed GCC 4.7 compatibility problems.
Changed min memory requirement for genome generation.

2.3.1o 04/13/2013
Fixed a bug with comma separated lists of input files.

2.3.1n 04/30/2013
Replaced incorretly released 2.3.1m.

2.3.1m 04/24/2013
Fixed a bug which in some cases caused problems with long reads.

2.3.1l 04/15/2013
Fixed a problem with --readFilesCommand.

2.3.1k 04/15/2013
Fixed chimeric output for single-end reads.
Fixed a problem with --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 settings.

2.3.1j 04/11/2013
Allowed spaces in paths: paths that contain spaces should be quoted with " ". Thanks for Tyler Hyndman for suggesting this patch.

2.3.1i 04/10/2013
Fixed problems with overflowing SJ buffer, new input parameters: --limitOutSJcollapsed, --limitOutSJoneRead.

2.3.1h 04/02/2013
Prevent output of strangely overlapping mates as chimeras.
Report error if --sjdbOverhang=0 with set --sjdbFileChrStartEnd or --sjdbGTFfile.

2.3.1g 03/29/2013
Implemented detection of proximal same-strand chimeras. Now it is possible to detect circular RNA (conisdered "chimeric").
More accurate treatment of overlapping mates.

2.3.1f 03/21/2013
New option --outSAMorder PairedKeepInputOrder to output alignments in the same order as they appear in the input FASTQ/A files.

2.3.1e 03/18/2013
Fixed possible problems with multi-threaded runs for small files which could have caused empty Chimeric.* and Unmapped.* output on some systems.

2.3.1d 03/17/2013
New option --outSAMprimaryFlag AllBestScore for marking all alignments with the best score as primary.
New parameter --limitOutSAMoneReadBytes 100000, limits the size of one SAM entry - important when a large number of multimappers is recorded.
Fixed a possible problem with Unmapped.* and Chimeric.* output which could generate empty or truncated output on some systems.
Coded a safer removal of the temporary directory _tmp which could have failed on some systems.
Fixed a bug which resulted in unexpected behavior for alignIntronMax < 7.

2.3.1c 03/01/2013
Fixed a bug which duplicated output in Chimeric.* and Unmapped.* when --outFilterType BySJout option is used.

2.3.1b 02/28/2013
Fixed possible issue which in some cases could have resulted in empty Chimeric.out.*

2.3.1a 02/25/2013
Fixed incorrect processing of --sjdbGTFchrPrefix.

2.3.0e

