[med-svn] [seqan] 14/14: More spelling issues
Andreas Tille
tille at debian.org
Wed Jan 20 10:39:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqan.
commit 3b1e9267f994d2f5cea873333475834d47a0d614
Author: Andreas Tille <tille at debian.org>
Date: Wed Jan 20 11:22:10 2016 +0100
More spelling issues
---
debian/patches/spelling.patch | 115 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 115 insertions(+)
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..647b5dd
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,115 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 18 Jan 2016 15:00:43 +0100
+Description: Fix some spelling issues
+
+--- a/apps/rabema/rabema_evaluate.cpp
++++ b/apps/rabema/rabema_evaluate.cpp
+@@ -91,7 +91,7 @@ public:
+ // original position of this read.
+ bool oracleMode;
+
+- // Consider only reads that have a unique match in the mapping result file. Usefull for precision computation.
++ // Consider only reads that have a unique match in the mapping result file. Useful for precision computation.
+ bool onlyUniqueReads;
+
+ // The benchmark category, one of {"all", "any-best", "all-best"}.
+@@ -142,7 +142,7 @@ public:
+ // Print the missed intervals to stderr for debugging purposes.
+ bool showMissedIntervals;
+
+- // Print superflous intervals (intervals found in BAM file but have too bad score).
++ // Print superfluous intervals (intervals found in BAM file but have too bad score).
+ bool showSuperflousIntervals;
+
+ // Print additional intervals (intervals found in BAM with good score that are not in WIT file).
+@@ -1093,7 +1093,7 @@ parseCommandLine(RabemaEvaluationOptions
+ "sample position. For simulated data."));
+ addOption(parser, seqan::ArgParseOption("", "only-unique-reads",
+ "Consider only reads that a single alignment in the mapping result file. "
+- "Usefull for precision computation."));
++ "Useful for precision computation."));
+ addOption(parser, seqan::ArgParseOption("", "match-N", "When set, N matches all characters without penalty."));
+ addOption(parser, seqan::ArgParseOption("", "distance-metric",
+ "Set distance metric. Valid values: hamming, edit. Default: edit.",
+@@ -1278,7 +1278,7 @@ int main(int argc, char const ** argv)
+ << " additional " << yesNo(options.showAdditionalIntervals) << '\n'
+ << " hit " << yesNo(options.showHitIntervals) << '\n'
+ << " missed " << yesNo(options.showMissedIntervals) << '\n'
+- << " superflous " << yesNo(options.showSuperflousIntervals) << '\n'
++ << " superfluous " << yesNo(options.showSuperflousIntervals) << '\n'
+ << " try hit " << yesNo(options.showTryHitIntervals) << '\n'
+ << "\n";
+
+@@ -1430,7 +1430,7 @@ int main(int argc, char const ** argv)
+ if (!empty(options.outTsvPath))
+ {
+ std::cerr << '\n'
+- << "Writting output TSV " << options.outTsvPath << " ...";
++ << "Writing output TSV " << options.outTsvPath << " ...";
+ std::ofstream tsvOut(toCString(options.outTsvPath), std::ios::out | std::ios::binary);
+ bool failed = false;
+ if (!tsvOut.good())
+--- a/util/py_lib/seqan/dox/validation.py
++++ b/util/py_lib/seqan/dox/validation.py
+@@ -97,7 +97,7 @@ class ReturnVoidValidator(ProcDocValidat
+ return # Skip if type has no returns member.
+ for r in proc_entry.returns:
+ if r.type == 'void':
+- msg = '@return superflous for "void" type -- simply show "void" in signature.'
++ msg = '@return superfluous for "void" type -- simply show "void" in signature.'
+ self.msg_printer.printTokenError(r.raw.first_token, msg, 'warning')
+
+
+--- a/apps/razers3/razers.cpp
++++ b/apps/razers3/razers.cpp
+@@ -437,7 +437,7 @@ void setUpArgumentParser(ArgumentParser
+ addOption(parser, ArgParseOption("mf", "mismatch-file", "Write mismatch patterns to \\fIFILE\\fP.", ArgParseOption::STRING, "FILE"));
+
+ addSection(parser, "Misc Options");
+- addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply compaction treshold by this value after reaching and compacting.", ArgParseOption::DOUBLE));
++ addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply compaction threshold by this value after reaching and compacting.", ArgParseOption::DOUBLE));
+ setMinValue(parser, "compact-mult", "0");
+ setDefaultValue(parser, "compact-mult", options.compactMult);
+ addOption(parser, ArgParseOption("ncf", "no-compact-frac", "Don't compact if in this last fraction of genome.", ArgParseOption::DOUBLE));
+--- a/apps/samcat/README
++++ b/apps/samcat/README
+@@ -6,7 +6,7 @@ SYNOPSIS
+
+ DESCRIPTION
+ This tool reads a set of input files in SAM or BAM format and outputs the concatenation of them. If the output
+- file name is ommitted the result is written to standard output in SAM format.
++ file name is omitted the result is written to standard output in SAM format.
+
+ (c) Copyright 2014 by David Weese.
+
+--- a/apps/samcat/samcat.cpp
++++ b/apps/samcat/samcat.cpp
+@@ -174,7 +174,7 @@ parseCommandLine(AppOptions & options, i
+ addDescription(parser, "This tool reads a set of input files in SAM format "
+ #endif
+ "and outputs the concatenation of them. "
+- "If the output file name is ommitted the result is written to stdout.");
++ "If the output file name is omitted the result is written to stdout.");
+
+ addDescription(parser, "(c) Copyright in 2014 by David Weese.");
+
+--- a/apps/seqan_flexbar/seqan_flexlib.cpp
++++ b/apps/seqan_flexbar/seqan_flexlib.cpp
+@@ -141,7 +141,7 @@ void ArgumentParserBuilder::addGeneralOp
+ }
+
+ seqan::ArgParseOption adInfoOpt = seqan::ArgParseOption(
+- "ni", "noInfo", "Don't print paramter overwiev to console.");
++ "ni", "noInfo", "Don't print parameter overwiev to console.");
+ addOption(parser, adInfoOpt);
+ }
+
+@@ -1746,7 +1746,7 @@ int flexbarMain(int argc, char const **
+ if (seqan::isSet(parser, "s") && (!seqan::isSet(parser, "u") || processingParams.uncalled == 0))
+ {
+ std::cout << "\nWarning: Substitute for uncalled bases is set, but will be ineffective unless number of allowed"
+- << " uncalled bases is set to a value higher than 0 by using the paramter -u [VALUE]\n";
++ << " uncalled bases is set to a value higher than 0 by using the parameter -u [VALUE]\n";
+ return 1;
+ }
+ getOptionValue(processingParams.trimLeft, parser, "tl");
--
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