[med-svn] [seqan] 03/03: Revert "More spelling issues"
Andreas Tille
tille at debian.org
Tue Jul 26 07:09:28 UTC 2016
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tille pushed a commit to branch master
in repository seqan.
commit b539505f3d6b9b8d76e478322d87f04637a1590c
Author: Andreas Tille <tille at debian.org>
Date: Tue Jul 26 09:08:48 2016 +0200
Revert "More spelling issues"
This reverts commit 3b1e9267f994d2f5cea873333475834d47a0d614.
---
debian/patches/spelling.patch | 115 ------------------------------------------
1 file changed, 115 deletions(-)
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 647b5dd..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-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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