Releases: alexdobin/STAR
Releases · alexdobin/STAR
2.6.1c minor bug fix
STAR 2.6.1c 2018/10/17
- Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.
2.6.1b
2.6.1a
STAR 2.6.1a 2018/08/14
- Process substitution can now be used with zipped VCF files, e.g. --varVCFfile <(zcat vcf.gz)
- Implemented fatal error exception if no SNPs are found in VCF files.
- Implemented --chimOutJunctionFormat 1 option to output some metadata (command lines and basic mapping statistics) at the end of Chimeric.out.junction file.
- The default value of --peOverlapMMp is reduced to 0.01 for less aggressive mate merging.
- Fixed the problem with control characters (ASCII<32) in genome and input read sequences. They used to be converted to N, now they are removed.
- Fixed a bug that caused serious problems with --sjdbInsertSave All option.
- Fixed a bug in merging mates (--peOverlap*) algorithm that was causing rare seg-faults.
- Fixed the GtstrandBit problem.
- Fixed a bug with multiple RG lines when inputting reads in SAM format.
- Fixed a bug causing seg-faults with shared memory and --outStd options.
- Fixed a bug with --outTmpDir and fifo files.
2.6.0c
STAR 2.6.0c 2018/05/10
- Fixed bugs in merging mates (--peOverlap*) and WASP filtering algorithms. Please see CHANGES and RELEASEnotes from 2.6.0a below.
STAR 2.6.0b 2018/05/02
- Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.6.0a below.
STAR 2.6.0a 2018/04/23
Major new features:
- Merging and mapping of overlapping paired-end reads with new options --peOverlapNbasesMin and --peOverlapMMp. The developmment of this algorithm was supported by Illumina, Inc. Many thanks to June Snedecor, Xiao Chen, and Felix Schlesinger for their extensive help in developing this feature.
- --varVCFfile option to input variant VCF file.
- New SAM attributes in the --outSAMattributes, vG, vA, and vW to report variants overlapping alignments.
- --waspOutputMode option for filtering allele specific alignments. This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061–1063 (2015), https://www.nature.com/articles/nmeth.3582 . Many thanks to Bryce van de Geijn for fruitful discussions.
- Detection of multimapping chimeras, with new options --chimMultimapNmax, --chimMultimapScoreRange and --chimNonchimScoreDropMin . Many thanks to Brian Haas for testing and feedback.
Minor new features:
- --alignInsertionFlush option which defines how to flush ambiguous insertion positions: None: old method, insertions are not flushed; Right: insertions are flushed to the right.
- --outSAMtlen option to select the calculation method for the TLEN field in the SAM/BAM files.
- --outBAMsortingBinsN option to control the number of sorting bins. Increasing this number reduces the amount of RAM required for sorting.
2.5.4b
2.5.4a
STAR 2.5.4a 2018/01/23
New features:
- Implemented read group ID output as the last column of the Chimeric.out.junction file.
- Implemented --readFilesPrefix option for specifying prefix (e.g. directory path) for the file names in --readFilesIn .
- Implemented standard SAM attribute "MC" to output the mate's CIGAR. Add MC to the list of attributes in the --outSAMattribute option.
- Implemented the ability to input the reads from unmapped SAM/BAM file: --readFilesType SAM SE[PE] for single-end [paired-end] reads to read from the SAM file specified, as usual in --readFilesIn. For BAM files, in addition, specify --readFilesCommand samtools view -h .
- Implemented --seedSplitMin option which was previously hardcoded at 12. his will allow mapping of mates shorter than 12nt.
- Implemented --outFilterIntronStrands None option to switch off filtering by strand consistency of junctions.
- Added new scripts extras/scripts/mergeLogFinal.awk,mergeSuperContig.awk,sjMotif.m
Bug fixes:
- Fixed a bug in chimeric detection code which sometimes led to uninitialized memory access. The chimeric output may change for a very small number of reads.
- Fixed a problem with --alignEndsProtrude implementation which prevented the output of alignments with protruded ends.
- Fixed a bug which set non-primary bit 0x100 in the SAM FLAG for unmapped mates.
- Fixed a bug in liftOver command that output an extra field in the GTF file.
- Fixed a problem that can arise for very small genomes while using --alignIntronMax 1.
2.5.3a
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Implemented --genomeFileSizes option to supply sizes of the genome index files. This allows for streaming of index files.
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Implemented extra references input in the SAM/AM header from user-created "extraReferences.txt" file in the genome directory.
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Implemented --chimOutType HardClip OR SoftClip options to output hard (default) / soft clipping in the BAM CIGAR for supplementary chimeric alignments.
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Implemented --chimMainSegmentMultNmax parameters, which may be used to prohibit chimeric alignments with multimapping main segments to reduce false positive chimeras.
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Implemented new SAM attribute 'ch' to mark chimeric aligmments in the BAM file for --chimOutType WithinBAM option.
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Implemented --bamRemoveDuplicatesType UniqueIdenticalNotMulti option, which (unlike the UniqueIdentical optipon) will NOT mark multi-mappers as duplicates.
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For --bamRemoveDuplicatesType UniqueIdentical, the unmmapped reads are no longer marked as duplicates.
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Fixed occasional seg-faults after the completion of the mapping runs with shared memory.
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Fixed a problem with RNEXT field in the Chimeric.out.sam file: RNEXT now always points to the other mate start.
2.5.2b
- Fixed a problem with --outSAMmultNmax 1 not working for transcriptomic output.
- Fixed a bug with chimeric BAM output for --chimOutType WithinBAM option.
- Fixed a bug that could cause non-stable BAM sorting if the gcc qsort is unstable.
- Fixed a bug with causing seg-faults when combining --twopassMode Basic --outSAMorder PairedKeepInputOrder .
- Fixed a problem with SAM header in cases where reference sequences are added at the mapping stage.
2.5.2a
- Fixed the "GstrandBit" problem.
- Fixed a bug introduced in 2.5.1a that caused problems with single-end alignments output in some cases.
- Fixed a bug that can cause STARlong seg-faults in rare cases.
- Fixed a bug that caused output of unmapped mates for single end alignments even with --outSAMunmapped None .
- Implemented --winReadCoverageRelativeMin and --winReadCoverageBasesMin to control coverage of the alignment windows for STARlong.
- Implemented --outSAMfilter KeepAllAddedReferences option which will keep all alignments to the added references.
- Implemented --alignEndsProtrude option to control output of alignments with protruding ends.
- Implemented --outTmpKeep All option to keep the temporary files.
- Implemented --alignEndsType Extend5pOfReads12 option for full extension of 5' ends of both mates.