New upstream version 2.6.1a+dfsg (ecb17f91) · Commits · Debian Med / rna-star

CHANGES.md

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		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.

		STAR 2.6.0c 2018/05/10
		======================

README.md

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		@@ -41,6 +41,7 @@ cd STAR-2.6.0a

		# Alternatively, get STAR source using git
		git clone https://github.com/alexdobin/STAR.git
		```

		Compile under Linux
		-------------------

doc/STARmanual.pdf

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extras/doc-latex/STARmanual.tex

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		@@ -34,7 +34,7 @@

		\newcommand{\sechyperref}[1]{\hyperref[#1]{Section \ref{#1}. \nameref{#1}}}

		\title{STAR manual 2.6.0a}
		\title{STAR manual 2.6.1a}
		\author{Alexander Dobin\\
		dobin@cshl.edu}
		\maketitle
		@@ -273,7 +273,7 @@ The SAM attributes can be specified by the user using \opt{outSAMattributes} \op
		\item[]
		\optv{NH HI NM MD} have standard meaning as defined in the SAM format specifications.
		\item[]
		\optv{AS} id the local alignment score (paired for paired-edn reads).
		\optv{AS} id the local alignment score (paired for paired-end reads).
		\item[]
		\optv{nM} is the number of mismatches per (paired) alignment, not to be confused with \optv{NM}, which is the number of mismatches in each mate.
		\item[]
		@@ -335,11 +335,11 @@ STAR-Fusion is a software package for detecting fusion transcript from STAR chim
		Chimeric alignments can be included together with normal alignments in the main (sorted or unsorted) BAM file(s) using \opt{chimOutType} \optv{WithinBAM}. In these files, formatting of chimeric alignments follows the latest SAM/BAM specifications.

		\subsection{Chimeric alignments in \ofilen{Chimeric.out.sam} .}
		When chimeric detection is switched on, STAR will output normal alignments into \ofilen{Aligned.*.sam/bam}, and will output chimeric alignments into a separate file \ofilen{Chimeric.out.sam}.
		With \opt{chimOutType} \optv{SeparateSAMold} STAR will output normal alignments into \ofilen{Aligned.*.sam/bam}, and will output chimeric alignments into a separate file \ofilen{Chimeric.out.sam}. Note that this option will be deprecated in the future, and the \opt{chimOutType} \optv{WithinBAM} is strongly recommended.
		Some reads may be output to both normal SAM/BAM files, and \ofilen{Chimeric.out.sam} for the following reason. STAR will output a non-chimeric alignment into \ofilen{Aligned.out.sam} with soft-clipping a portion of the read. If this portion is long enough, and it maps well and uniquely somewhere else in the genome, there will also be a chimeric alignment output into \ofilen{Chimeric.out.sam}. For instance, if you have a paired-end read where the second mate can be split chimerically into 70 and 30 bases. The 100b of the first mate + 70b of the 2nd mate map non-chimerically,and the mapping length/score are big enough, so they will be output into \ofilen{Aligned.out.sam} file. At the same time, the chimeric segments 100-mate1 + 70-mate2 and 30-mate2 will be output into \ofilen{Chimeric.out.sam}.

		\subsection{Chimeric alignments in \ofilen{Chimeric.out.junction}}
		In addition to \ofilen{Chimeric.out.sam}, STAR will generate \ofilen{Chimeric.out.junction} file which maybe more convenient for downstream analysis.
		By default, or with \opt{chimOutType} \optv{Junctions}, STAR will generate \ofilen{Chimeric.out.junction} file which maybe more convenient for downstream analysis.
		The format of this file is as follows. Every line contains one chimerically aligned read, e.g.:
		\begin{verbatim}
		chr22 23632601 + chr9 133729450 + 1 0 0

extras/doc-latex/parametersDefault.tex

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		@@ -637,7 +637,7 @@
		\optValue{0}
		\optLine{int{\textgreater}=0: minimum number of overlap bases to trigger mates merging and realignment}
		\optName{peOverlapMMp}
		\optValue{0.1}
		\optValue{0.01}
		\optLine{real, {\textgreater}=0 {\&} {\textless}1: maximum proportion of mismatched bases in the overlap area}
		\end{optTable}
		\optSection{Windows, Anchors, Binning}\label{Windows,_Anchors,_Binning}
		@@ -716,6 +716,13 @@
		\optName{chimNonchimScoreDropMin}
		\optValue{20}
		\optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read lenght has to be smaller than this value}
		\optName{chimOutJunctionFormat}
		\optValue{0}
		\optLine{int: formatting type for the Chimeric.out.junction file}
		\begin{optOptTable}
		\optOpt{0} \optOptLine{no comment lines/headers}
		\optOpt{1} \optOptLine{comment lines at the end of the file: command line and Nreads: total, unique, multi}
		\end{optOptTable}
		\end{optTable}
		\optSection{Quantification of Annotations}\label{Quantification_of_Annotations}
		\begin{optTable}