[med-svn] [rna-star] 05/05: some spelling fixes
Sascha Steinbiss
satta at debian.org
Fri Jan 26 13:40:28 UTC 2018
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satta pushed a commit to branch master
in repository rna-star.
commit bef6974533f6fac5f1851dc9abe248c437d9dc2b
Author: Sascha Steinbiss <satta at debian.org>
Date: Fri Jan 26 14:29:43 2018 +0100
some spelling fixes
---
debian/changelog | 1 +
debian/patches/series | 1 +
debian/patches/spelling.patch | 93 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 95 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 87c8249..46188cc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ rna-star (2.5.4a+dfsg-1) unstable; urgency=medium
* d/control: Remove obsolete Testsuite entry.
* d/rules: Remove trailing whitespace.
* d/copyright: Use secure copyright format URL.
+ * Spelling fixes.
[ Steffen Moeller ]
* debian/upstream/metadata:
diff --git a/debian/patches/series b/debian/patches/series
index 6c3b15b..36bf732 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
donotuse_own_htslib.patch
mips_shm_noreserve.patch
reproducible.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..3cfade3
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,93 @@
+Description: spelling
+Author: Sascha Steinbiss <satta at debian.org>
+Forwarded: https://github.com/alexdobin/STAR/pull/369
+Last-Update: 2018-01-26
+--- a/extras/doc-latex/STARmanual.tex
++++ b/extras/doc-latex/STARmanual.tex
+@@ -72,7 +72,7 @@
+ }
+
+ \paragraph{Mac OS X.\newline}
+-Current versions of Mac OS X Xcode are shipped with Clang replacing the standard gcc compiler. Presently, standard Clang does not support OpenMP which creates problems for STAR compilation. One option to avoid this problem is to install gcc (preferrably using \code{homebrew} package manager). Another option is to add OpenMP functionality to Clang.
++Current versions of Mac OS X Xcode are shipped with Clang replacing the standard gcc compiler. Presently, standard Clang does not support OpenMP which creates problems for STAR compilation. One option to avoid this problem is to install gcc (preferably using \code{homebrew} package manager). Another option is to add OpenMP functionality to Clang.
+
+ \subsection{Basic workflow.}
+ Basic STAR workflow consists of 2 steps:
+--- a/extras/doc-latex/parametersDefault.tex
++++ b/extras/doc-latex/parametersDefault.tex
+@@ -8,7 +8,7 @@
+ \begin{optTable}
+ \optName{sysShell}
+ \optValue{-}
+- \optLine{string: path to the shell binary, preferrably bash, e.g. /bin/bash.}
++ \optLine{string: path to the shell binary, preferably bash, e.g. /bin/bash.}
+ \begin{optOptTable}
+ \optOpt{-} \optOptLine{the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.}
+ \end{optOptTable}
+@@ -344,7 +344,7 @@
+ \begin{optTable}
+ \optName{bamRemoveDuplicatesType}
+ \optValue{-}
+- \optLine{string: mark duplicates in the BAM file, for now only works with (i) sorted BAM feeded with inputBAMfile, and (ii) for paired-end alignments only}
++ \optLine{string: mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only}
+ \begin{optOptTable}
+ \optOpt{-} \optOptLine{no duplicate removal/marking}
+ \optOpt{UniqueIdentical} \optOptLine{mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical}
+@@ -635,7 +635,7 @@
+ \optLine{int{\textgreater}=0: minimum total (summed) score of the chimeric segments}
+ \optName{chimScoreDropMax}
+ \optValue{20}
+- \optLine{int{\textgreater}=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segements) from the read length}
++ \optLine{int{\textgreater}=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length}
+ \optName{chimScoreSeparation}
+ \optValue{10}
+ \optLine{int{\textgreater}=0: minimum difference (separation) between the best chimeric score and the next one}
+--- a/source/parametersDefault
++++ b/source/parametersDefault
+@@ -10,7 +10,7 @@
+
+ ### System
+ sysShell -
+- string: path to the shell binary, preferrably bash, e.g. /bin/bash.
++ string: path to the shell binary, preferably bash, e.g. /bin/bash.
+ - ... the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.
+
+ ### Run Parameters
+@@ -309,7 +309,7 @@
+ ### BAM processing
+
+ bamRemoveDuplicatesType -
+- string: mark duplicates in the BAM file, for now only works with (i) sorted BAM feeded with inputBAMfile, and (ii) for paired-end alignments only
++ string: mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only
+ - ... no duplicate removal/marking
+ UniqueIdentical ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical
+ UniqueIdenticalNotMulti ... mark duplicate unique mappers but not multimappers.
+@@ -565,7 +565,7 @@
+ int>=0: minimum total (summed) score of the chimeric segments
+
+ chimScoreDropMax 20
+- int>=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segements) from the read length
++ int>=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length
+
+ chimScoreSeparation 10
+ int>=0: minimum difference (separation) between the best chimeric score and the next one
+--- a/source/Genome.cpp
++++ b/source/Genome.cpp
+@@ -516,7 +516,7 @@
+ P->winBinNbits = (uint) floor( log2( max( max(4LLU,P->alignIntronMax), (P->alignMatesGapMax==0 ? 1000LLU : P->alignMatesGapMax) ) /4 ) + 0.5);
+ P->winBinNbits = max( P->winBinNbits, (uint) floor(log2(P->nGenome/40000+1)+0.5) );
+ //ISSUE - to be fixed in STAR3: if alignIntronMax>0 but alignMatesGapMax==0, winBinNbits will be defined by alignIntronMax
+- P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" redefined winBinNbits="<< P->winBinNbits <<endl;
++ P->inOut->logMain << "To accommodate alignIntronMax="<<P->alignIntronMax<<" redefined winBinNbits="<< P->winBinNbits <<endl;
+ };
+
+ if (P->winBinNbits > P->genomeChrBinNbits) {
+@@ -531,7 +531,7 @@
+ //redefine winFlankNbins,winAnchorDistNbins
+ P->winFlankNbins=max(P->alignIntronMax,P->alignMatesGapMax)/(1LLU<<P->winBinNbits)+1;
+ P->winAnchorDistNbins=2*P->winFlankNbins;
+- P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" and alignMatesGapMax="<<P->alignMatesGapMax<<\
++ P->inOut->logMain << "To accommodate alignIntronMax="<<P->alignIntronMax<<" and alignMatesGapMax="<<P->alignMatesGapMax<<\
+ ", redefined winFlankNbins="<<P->winFlankNbins<<" and winAnchorDistNbins="<<P->winAnchorDistNbins<<endl;
+ };
+
--
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