2.7.0d

alexdobin · Feb 19, 2019 · 09d7f77 · 09d7f77
1 parent a42a589
commit 09d7f77
Show file tree

Hide file tree

Showing 7 changed files with 12 additions and 5 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,4 +1,4 @@
-STAR 2.7.0d 2019/02/18
+STAR 2.7.0d 2019/02/19
 ======================
 * Implemented --soloBarcodeReadLength option for barcode read length not equal to the UMI+CB length
 * Enforced genome version rules for 2.7.0

diff --git a/bin/MacOSX_x86_64/STAR b/bin/MacOSX_x86_64/STAR
diff --git a/bin/MacOSX_x86_64/STARlong b/bin/MacOSX_x86_64/STARlong
diff --git a/doc/STARmanual.pdf b/doc/STARmanual.pdf
diff --git a/extras/doc-latex/STARmanual.tex b/extras/doc-latex/STARmanual.tex
@@ -34,7 +34,7 @@
 
 \newcommand{\sechyperref}[1]{\hyperref[#1]{Section \ref{#1}. \nameref{#1}}}
 
-\title{STAR manual 2.7.0a}
+\title{STAR manual 2.7.0d}
 \author{Alexander Dobin\\
 dobin@cshl.edu}
 \maketitle

diff --git a/extras/doc-latex/convertParDefToLatexTable.awk b/extras/doc-latex/convertParDefToLatexTable.awk
@@ -36,7 +36,7 @@ if ($1=="###") {# new group/subsection of parameters
   nOpt=0;
   while ($1!="") {
       $0=substr($0,match($0,/[^[:space:]]/));
-      no=split($0,oo,/[:space:]*\.\.\.[:space:]*/);
+      no=split($0,oo,/[[:space:]]*\.\.\.[[:space:]]*/);
       if (no!=2) {# not option line
            if (nOpt>0) print optOptTableEnd;
            print "  \\optLine{" $0 "}" " ";

diff --git a/extras/doc-latex/parametersDefault.tex b/extras/doc-latex/parametersDefault.tex
@@ -808,6 +808,13 @@
 \optName{soloUMIlen}
   \optValue{10}
   \optLine{int{\textgreater}0: UMI length} 
+\optName{soloBarcodeReadLength}
+  \optValue{1}
+  \optLine{int: length of the barcode read} 
+\begin{optOptTable}
+  \optOpt{1}   \optOptLine{equal to sum of soloCBlen+soloUMIlen}
+  \optOpt{0}   \optOptLine{not defined, do not check}
+\end{optOptTable}
 \optName{soloStrand}
   \optValue{Forward}
   \optLine{string: strandedness of the solo libraries:} 
@@ -836,8 +843,8 @@
   \optLine{string(s)               file names for STARsolo output} 
 \begin{optOptTable}
   \optOpt{1st word}   \optOptLine{file name prefix}
-  \optOpt{2nd word}   \optOptLine{barcode sequences}
-  \optOpt{3rd word}   \optOptLine{gene IDs and names}
+  \optOpt{2nd word}   \optOptLine{gene IDs and names}
+  \optOpt{3rd word}   \optOptLine{barcode sequences}
   \optOpt{4th word}   \optOptLine{cell/gene counts matrix}
   \optOpt{5th word}   \optOptLine{cell/splice junction counts matrix}
 \end{optOptTable}