[med-svn] [seqan2] 02/05: spelling
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Oct 9 09:59:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository seqan2.
commit 1c4890645d271c51a636f6b4989c7783b87d23a0
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Sun Oct 9 02:29:56 2016 -0700
spelling
---
debian/patches/spelling.patch | 651 +++++++++++++++++++++++++++++-------------
1 file changed, 460 insertions(+), 191 deletions(-)
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index ca67bb9..bc4e414 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -1,10 +1,10 @@
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:
+Forwarded: https://github.com/seqan/seqan/pull/1872
+--- seqan2.orig/apps/rabema/rabema_evaluate.cpp
++++ seqan2/apps/rabema/rabema_evaluate.cpp
+@@ -91,7 +91,7 @@
// original position of this read.
bool oracleMode;
@@ -13,7 +13,7 @@ Description: Fix some spelling issues
bool onlyUniqueReads;
// The benchmark category, one of {"all", "any-best", "all-best"}.
-@@ -142,7 +142,7 @@ public:
+@@ -142,7 +142,7 @@
// Print the missed intervals to stderr for debugging purposes.
bool showMissedIntervals;
@@ -22,7 +22,7 @@ Description: Fix some spelling issues
bool showSuperflousIntervals;
// Print additional intervals (intervals found in BAM with good score that are not in WIT file).
-@@ -1093,7 +1093,7 @@ parseCommandLine(RabemaEvaluationOptions
+@@ -1093,7 +1093,7 @@
"sample position. For simulated data."));
addOption(parser, seqan::ArgParseOption("", "only-unique-reads",
"Consider only reads that a single alignment in the mapping result file. "
@@ -31,7 +31,7 @@ Description: Fix some spelling issues
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)
+@@ -1278,7 +1278,7 @@
<< " additional " << yesNo(options.showAdditionalIntervals) << '\n'
<< " hit " << yesNo(options.showHitIntervals) << '\n'
<< " missed " << yesNo(options.showMissedIntervals) << '\n'
@@ -40,7 +40,7 @@ Description: Fix some spelling issues
<< " try hit " << yesNo(options.showTryHitIntervals) << '\n'
<< "\n";
-@@ -1430,7 +1430,7 @@ int main(int argc, char const ** argv)
+@@ -1430,7 +1430,7 @@
if (!empty(options.outTsvPath))
{
std::cerr << '\n'
@@ -49,9 +49,9 @@ Description: Fix some spelling issues
std::ofstream tsvOut(toCString(options.outTsvPath), std::ios::out | std::ios::binary);
bool failed = false;
if (!tsvOut.good())
---- a/apps/razers3/razers.cpp
-+++ b/apps/razers3/razers.cpp
-@@ -437,7 +437,7 @@ void setUpArgumentParser(ArgumentParser
+--- seqan2.orig/apps/razers3/razers.cpp
++++ seqan2/apps/razers3/razers.cpp
+@@ -437,7 +437,7 @@
addOption(parser, ArgParseOption("mf", "mismatch-file", "Write mismatch patterns to \\fIFILE\\fP.", ArgParseOption::STRING, "FILE"));
addSection(parser, "Misc Options");
@@ -60,9 +60,9 @@ Description: Fix some spelling issues
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
+--- seqan2.orig/apps/samcat/README
++++ seqan2/apps/samcat/README
+@@ -6,7 +6,7 @@
DESCRIPTION
This tool reads a set of input files in SAM or BAM format and outputs the concatenation of them. If the output
@@ -71,9 +71,9 @@ Description: Fix some spelling issues
(c) Copyright 2014 by David Weese.
---- a/apps/samcat/samcat.cpp
-+++ b/apps/samcat/samcat.cpp
-@@ -174,7 +174,7 @@ parseCommandLine(AppOptions & options, i
+--- seqan2.orig/apps/samcat/samcat.cpp
++++ seqan2/apps/samcat/samcat.cpp
+@@ -174,7 +174,7 @@
addDescription(parser, "This tool reads a set of input files in SAM format "
#endif
"and outputs the concatenation of them. "
@@ -82,9 +82,18 @@ Description: Fix some spelling issues
addDescription(parser, "(c) Copyright in 2014 by David Weese.");
---- a/apps/fiona/compute_gain.cpp
-+++ b/apps/fiona/compute_gain.cpp
-@@ -1124,7 +1124,7 @@ int main(int argc, char const ** argv)
+--- seqan2.orig/apps/fiona/compute_gain.cpp
++++ seqan2/apps/fiona/compute_gain.cpp
+@@ -111,7 +111,7 @@
+ // Number of errors pre-correction/post-correction.
+ uint64_t numErrorsPre;
+ uint64_t numErrorsPost;
+- // Number of errorneous reads pre-correction/post-correction.
++ // Number of erroneous reads pre-correction/post-correction.
+ uint64_t numErrorReadsPre;
+ uint64_t numErrorReadsPost;
+ uint64_t numReads;
+@@ -1124,7 +1124,7 @@
std::cerr << "WARNING: Files not read completely!\n";
if (error)
{
@@ -93,9 +102,9 @@ Description: Fix some spelling issues
return 1;
}
---- a/apps/fiona/fiona.cpp
-+++ b/apps/fiona/fiona.cpp
-@@ -2609,20 +2609,20 @@ double medianLevel(Iter<TIndex, VSTree<T
+--- seqan2.orig/apps/fiona/fiona.cpp
++++ seqan2/apps/fiona/fiona.cpp
+@@ -2609,20 +2609,20 @@
double median = 0.0;
double mediumTotalOccs = 0.0;
@@ -119,7 +128,7 @@ Description: Fix some spelling issues
{
sumMedian += iterMap->second*iterMap->first;
if (sumMedian >= mediumTotalOccs)
-@@ -4199,7 +4199,7 @@ unsigned correctReads(
+@@ -4199,7 +4199,7 @@
String<double> sd;
standardDeviation(sd, store.readSeqStore, options.genomeLength);
@@ -128,9 +137,18 @@ Description: Fix some spelling issues
for (unsigned i = 0; i < length(options.expectedTheoretical); ++i)
{
double expectedTemporary = options.expectedTheoretical[i] - options.strictness * sd[i];
---- a/apps/mason2/README.mason_splicing
-+++ b/apps/mason2/README.mason_splicing
-@@ -19,7 +19,7 @@ Table of Contents
+@@ -5268,7 +5268,7 @@
+ // Parallelization Options.
+ addSection(parser, "Parallelization Options");
+
+- addOption(parser, seqan::ArgParseOption("nt", "num-threads", "Number of threds to use (default 1).",
++ addOption(parser, seqan::ArgParseOption("nt", "num-threads", "Number of threads to use (default 1).",
+ seqan::ArgParseArgument::INTEGER, "INT"));
+ setMinValue(parser, "num-threads", "1");
+ setDefaultValue(parser, "num-threads", options.numThreads);
+--- seqan2.orig/apps/mason2/README.mason_splicing
++++ seqan2/apps/mason2/README.mason_splicing
+@@ -19,7 +19,7 @@
1. Overview
------------------------------------------------------------------------------
@@ -139,8 +157,8 @@ Description: Fix some spelling issues
reference sequence and an optional variant file.
------------------------------------------------------------------------------
---- a/apps/ngs_roi/project_spliced.h
-+++ b/apps/ngs_roi/project_spliced.h
+--- seqan2.orig/apps/ngs_roi/project_spliced.h
++++ seqan2/apps/ngs_roi/project_spliced.h
@@ -31,7 +31,7 @@
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
@@ -150,9 +168,9 @@ Description: Fix some spelling issues
// GTF/GFF intervals.
//
// This mode is enabled when the --gff-group-by KEY option is used. In this
---- a/apps/pair_align/pair_align.cpp
-+++ b/apps/pair_align/pair_align.cpp
-@@ -33,7 +33,7 @@ parseCommandLine(Options & options, int
+--- seqan2.orig/apps/pair_align/pair_align.cpp
++++ seqan2/apps/pair_align/pair_align.cpp
+@@ -33,7 +33,7 @@
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-s\\fP \\fIIN\\fP");
setCategory(parser, "Sequence Alignment");
addDescription(parser,
@@ -161,9 +179,9 @@ Description: Fix some spelling issues
"tweaking various parameters.");
addSection(parser, "Main Options");
---- a/apps/rabema/README
-+++ b/apps/rabema/README
-@@ -112,7 +112,7 @@ passed an error rate of 8% to the evalua
+--- seqan2.orig/apps/rabema/README
++++ seqan2/apps/rabema/README
+@@ -112,7 +112,7 @@
alignments. The number of additional hits is 0. This is the number of hits in
the read mapper output with a valid error rate (below 3% in this case) that
are not found in the gold standard. If this number is greater than zero then
@@ -172,16 +190,16 @@ Description: Fix some spelling issues
program. If you get such a number then please contact the Rabema authors.
The total number of reads is 8,840, the number of reads having an alignment
-@@ -136,4 +136,4 @@ reports generated by Rabema.
+@@ -136,4 +136,4 @@
Contact
------
- Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
\ No newline at end of file
+ Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
---- a/apps/rabema/rabema_build_gold_standard.cpp
-+++ b/apps/rabema/rabema_build_gold_standard.cpp
-@@ -986,7 +986,7 @@ parseCommandLine(BuildGoldStandardOption
+--- seqan2.orig/apps/rabema/rabema_build_gold_standard.cpp
++++ seqan2/apps/rabema/rabema_build_gold_standard.cpp
+@@ -986,7 +986,7 @@
"[\\fIOPTIONS\\fP] \\fB--out-gsi\\fP \\fIOUT.gsi\\fP \\fB--reference\\fP \\fIREF.fa\\fP "
"\\fB--in-bam\\fP \\fIPERFECT.{sam,bam}\\fP");
addDescription(parser,
@@ -190,8 +208,8 @@ Description: Fix some spelling issues
"and a perfect SAM/BAM map (e.g. created using RazerS 3 in full-sensitivity mode).");
addDescription(parser,
"The input SAM/BAM file must be \\fIsorted by coordinate\\fP. The program will create a "
---- a/apps/rabema/ref_id_mapping.h
-+++ b/apps/rabema/ref_id_mapping.h
+--- seqan2.orig/apps/rabema/ref_id_mapping.h
++++ seqan2/apps/rabema/ref_id_mapping.h
@@ -24,7 +24,7 @@
// file. The order in the BAM file might not be the same as in the FASTA
// file.
@@ -201,8 +219,8 @@ Description: Fix some spelling issues
// name store caches.
// ==========================================================================
---- a/apps/sak/README
-+++ b/apps/sak/README
+--- seqan2.orig/apps/sak/README
++++ seqan2/apps/sak/README
@@ -1,6 +1,6 @@
Swiss Army Knife tool... It slices and dices and makes the laundry!
@@ -211,9 +229,9 @@ Description: Fix some spelling issues
files. It supports all formats supported by the AutoSeqFormat class from
SeqAn, including FASTA, FASTQ and QSeq (Illumina format).
---- a/apps/seqcons2/seqcons.cpp
-+++ b/apps/seqcons2/seqcons.cpp
-@@ -92,7 +92,7 @@ int main(int argc, char const ** argv)
+--- seqan2.orig/apps/seqcons2/seqcons.cpp
++++ seqan2/apps/seqcons2/seqcons.cpp
+@@ -92,7 +92,7 @@
}
catch (std::runtime_error & e)
{
@@ -222,9 +240,9 @@ Description: Fix some spelling issues
<< " " << e.what() << "\n";
return 1;
}
---- a/dox/pages/index.dox
-+++ b/dox/pages/index.dox
-@@ -40,7 +40,7 @@ Alternatively you might want to check th
+--- seqan2.orig/dox/pages/index.dox
++++ seqan2/dox/pages/index.dox
+@@ -40,7 +40,7 @@
<tr><td><ul><li>@link localAlignment @endlink</li></ul></td><td></td></tr>
<tr><td><ul><li>@link LocalAlignmentEnumerator @endlink</li></ul></td><td>offers the Waterman-Eggert algorithm for enumerating suboptimal local alignments</td></tr>
<tr><td><ul><li>@link Align @endlink</li></ul></td><td>provides a data structure for tabular alignment of sequences with the same type</td></tr>
@@ -233,9 +251,9 @@ Description: Fix some spelling issues
</table>
</li>
<li>
---- a/dox/pages/language_entities.dox
-+++ b/dox/pages/language_entities.dox
-@@ -16,7 +16,7 @@ We call the above mentioned things like
+--- seqan2.orig/dox/pages/language_entities.dox
++++ seqan2/dox/pages/language_entities.dox
+@@ -16,7 +16,7 @@
@htmlonly <h2 data-lang-entity="typedef" id="typedef">Typedef</h2> @endhtmlonly
@@ -244,9 +262,9 @@ Description: Fix some spelling issues
When programming SeqAn, they are often used for giving short names to complicated, nested template instantiations or to the result of a <a href="#metafunction">metafunction</a>.
---- a/include/seqan/align/gaps_base.h
-+++ b/include/seqan/align/gaps_base.h
-@@ -112,7 +112,7 @@ typedef Tag<RightOfViewPos_> RightOfView
+--- seqan2.orig/include/seqan/align/gaps_base.h
++++ seqan2/include/seqan/align/gaps_base.h
+@@ -112,7 +112,7 @@
* @tparam TSequence The type of the underlying sequence.
* @tparam TSpec Tag for specialization.
*
@@ -255,9 +273,9 @@ Description: Fix some spelling issues
* an infix of the gapped sequence (clipping). The gaps are not inserted into the underlying sequence (source) but
* stored separately. Using the clipping is optional and meant for selecting parts of the alignment as a part of the
* result of a local alignment algorithm.
---- a/include/seqan/arg_parse/tool_doc.h
-+++ b/include/seqan/arg_parse/tool_doc.h
-@@ -568,7 +568,7 @@ public:
+--- seqan2.orig/include/seqan/arg_parse/tool_doc.h
++++ seqan2/include/seqan/arg_parse/tool_doc.h
+@@ -568,7 +568,7 @@
*
* @section Remarks
*
@@ -266,9 +284,9 @@ Description: Fix some spelling issues
* and represent all information related to a command line tool that would normally go into a man page. It can be
* printed to STL streams in different formats, currently plain text, HTML and man pages are supported.
*
---- a/include/seqan/basic/iterator_zip.h
-+++ b/include/seqan/basic/iterator_zip.h
-@@ -82,7 +82,7 @@ typedef Tag<ZipIterator_> ZipIterator;
+--- seqan2.orig/include/seqan/basic/iterator_zip.h
++++ seqan2/include/seqan/basic/iterator_zip.h
+@@ -82,7 +82,7 @@
* @tparam TIteratorTypes A template parameter pack with one or more @link ContainerConcept#Iterator @endlink types.
*
* This iterator ties together different iterator types for different containers of the same size.
@@ -277,9 +295,9 @@ Description: Fix some spelling issues
* Note, that all operations are still executed in a serial fashion.
* If the zip iterator is dereferenced it returns a <a href="http://en.cppreference.com/w/cpp/utility/tuple">std::tuple</a>
* containing the dereferenced values of all embedded iterators.
---- a/include/seqan/basic/metaprogramming_enable_if.h
-+++ b/include/seqan/basic/metaprogramming_enable_if.h
-@@ -252,7 +252,7 @@ struct DisableIf2<true, T> {};
+--- seqan2.orig/include/seqan/basic/metaprogramming_enable_if.h
++++ seqan2/include/seqan/basic/metaprogramming_enable_if.h
+@@ -252,7 +252,7 @@
* @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or a metafunction returning such a tag
* type. If <tt>True</tt> then the constructor is visible, otherwise, it is not.
*
@@ -288,7 +306,7 @@ Description: Fix some spelling issues
* href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must be used as the last dummy-argument of a constructor.
*
* To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -280,7 +280,7 @@ struct DisableIf2<true, T> {};
+@@ -280,7 +280,7 @@
* @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or a metafunction returning such a tag
* type. If <tt>False</tt> then the constructor is visible, otherwise, it is not.
*
@@ -297,7 +315,7 @@ Description: Fix some spelling issues
* href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must be used as the last dummy-argument of a constructor.
*
* To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -309,7 +309,7 @@ struct DisableIf2<true, T> {};
+@@ -309,7 +309,7 @@
* type. If <tt>True</tt> then the function is visible, otherwise, it is not.
* @param TResult The type that the function should have as the return type in case it is enabled.
*
@@ -306,7 +324,7 @@ Description: Fix some spelling issues
* href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must occur as the return type definition of the function.
*
* To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
-@@ -338,7 +338,7 @@ struct DisableIf2<true, T> {};
+@@ -338,7 +338,7 @@
* type. If <tt>False</tt> then the function is visible, otherwise, it is not.
* @param TResult The type that the function should have as the return type in case it is enabled.
*
@@ -315,9 +333,9 @@ Description: Fix some spelling issues
* href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must occur as the return type definition of the function.
*
* To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
---- a/include/seqan/index/index_esa_base.h
-+++ b/include/seqan/index/index_esa_base.h
-@@ -169,7 +169,7 @@ namespace seqan
+--- seqan2.orig/include/seqan/index/index_esa_base.h
++++ seqan2/include/seqan/index/index_esa_base.h
+@@ -169,7 +169,7 @@
typedef MaxRepeats_<void> MaxRepeats; // maximal repeat
struct MaxRepeatOccurrences;
typedef MaxRepeats_<MultiMems_> MultiMems; // Multiple Maximal Exact Match
@@ -326,7 +344,7 @@ Description: Fix some spelling issues
/*!
-@@ -197,7 +197,7 @@ namespace seqan
+@@ -197,7 +197,7 @@
template <typename TSize>
struct VertexEsa {
Pair<TSize> range; // current SA interval of hits (unique node identifier)
@@ -335,9 +353,9 @@ Description: Fix some spelling issues
VertexEsa() : range(0, 0), parentRight(0) {}
---- a/include/seqan/index/index_esa_stree.h
-+++ b/include/seqan/index/index_esa_stree.h
-@@ -335,7 +335,7 @@ SEQAN_CONCEPT_IMPL((Index<TText, IndexEs
+--- seqan2.orig/include/seqan/index/index_esa_stree.h
++++ seqan2/include/seqan/index/index_esa_stree.h
+@@ -335,7 +335,7 @@
typedef typename HistoryStack_<Iter>::Type TStack;
typedef Iter iterator;
@@ -346,9 +364,9 @@ Description: Fix some spelling issues
//____________________________________________________________________________
---- a/include/seqan/index/index_wotd.h
-+++ b/include/seqan/index/index_wotd.h
-@@ -323,7 +323,7 @@ SEQAN_CONCEPT_IMPL((Index<TText, IndexWo
+--- seqan2.orig/include/seqan/index/index_wotd.h
++++ seqan2/include/seqan/index/index_wotd.h
+@@ -323,7 +323,7 @@
TSize parentRepLen; // representative length of parent node
TSize edgeLen; // length of edge above current node
Pair<TSize> range; // current SA interval of hits
@@ -357,9 +375,9 @@ Description: Fix some spelling issues
VertexWotdModified_() :
node(0),
---- a/include/seqan/parallel/parallel_splitting.h
-+++ b/include/seqan/parallel/parallel_splitting.h
-@@ -58,7 +58,7 @@ typedef Tag<Equidistant_> Equidistant;
+--- seqan2.orig/include/seqan/parallel/parallel_splitting.h
++++ seqan2/include/seqan/parallel/parallel_splitting.h
+@@ -58,7 +58,7 @@
* to parallelize large for-loops that iterate over a contiguous range of elements. The interval and the number of
* subintervals can be set in the constructor @link Splitter::Splitter @endlink. @link Splitter#length @endlink and
* @link Splitter#resize @endlink can be used to retrieve or change the number of subintervals later. In contrast to
@@ -368,9 +386,9 @@ Description: Fix some spelling issues
* right boundary of each subinterval (see example code below).
*
* @section Examples
---- a/include/seqan/sequence/sequence_interface.h
-+++ b/include/seqan/sequence/sequence_interface.h
-@@ -1101,7 +1101,7 @@ _capacityReturned(T const &,
+--- seqan2.orig/include/seqan/sequence/sequence_interface.h
++++ seqan2/include/seqan/sequence/sequence_interface.h
+@@ -1101,7 +1101,7 @@
* @return TSize The amount of the requested capacity that was available. That is the function returns the minimum of
* <tt>newCapacity</tt> and <tt>capacity(me)</tt>.
*
@@ -379,9 +397,9 @@ Description: Fix some spelling issues
*
* Use @link StringConcept#resize @endlink if you want to change the size of a container.
*
---- a/include/seqan/sequence/string_set_base.h
-+++ b/include/seqan/sequence/string_set_base.h
-@@ -69,7 +69,7 @@ struct Owner {};
+--- seqan2.orig/include/seqan/sequence/string_set_base.h
++++ seqan2/include/seqan/sequence/string_set_base.h
+@@ -69,7 +69,7 @@
* chromosomes of a genome. This facilitates writing generic data structures and algorithms to operate on single
* strings and genomes which is captured by the @link TextConcept @endlink.
*
@@ -390,8 +408,8 @@ Description: Fix some spelling issues
* storing copies of strings and identifying strings by a common id.
*
* @section Examples
---- a/include/seqan/tabix_io/tabix_index_tbi.h
-+++ b/include/seqan/tabix_io/tabix_index_tbi.h
+--- seqan2.orig/include/seqan/tabix_io/tabix_index_tbi.h
++++ seqan2/include/seqan/tabix_io/tabix_index_tbi.h
@@ -33,7 +33,7 @@
// ==========================================================================
// (Read-only) Tabix index support.
@@ -401,9 +419,9 @@ Description: Fix some spelling issues
// related file, e.g. VCF, GFF, SAM, BED, etc. The corresponding file only
// needs to be sorted by chromosomal position in advance and optionally
// compressed with 'bgzip'. The resulting file must be indexed with 'tabix'.
---- a/manual/attic/Tutorial/IndicesOld.rst
-+++ b/manual/attic/Tutorial/IndicesOld.rst
-@@ -3,7 +3,7 @@ TOC
+--- seqan2.orig/manual/attic/Tutorial/IndicesOld.rst
++++ seqan2/manual/attic/Tutorial/IndicesOld.rst
+@@ -3,7 +3,7 @@
Indices
-------
@@ -412,9 +430,9 @@ Description: Fix some spelling issues
occurrences of a pattern in a string or a set of strings. Substring
indices are very efficient for the exact string matching problem, i.e.
finding all exact occurrences of a pattern in a text or a text
---- a/tests/basic/test_basic_allocator.h
-+++ b/tests/basic/test_basic_allocator.h
-@@ -49,7 +49,7 @@ using namespace seqan;
+--- seqan2.orig/tests/basic/test_basic_allocator.h
++++ seqan2/tests/basic/test_basic_allocator.h
+@@ -49,7 +49,7 @@
// ==========================================================================
// The following helper class is passed as the parent allocator to all tested
@@ -423,8 +441,8 @@ Description: Fix some spelling issues
// and checks whether all allocated memory blocks are correctly deallocated
// when it is destructed.
---- a/tests/realign/test_realign.cpp
-+++ b/tests/realign/test_realign.cpp
+--- seqan2.orig/tests/realign/test_realign.cpp
++++ seqan2/tests/realign/test_realign.cpp
@@ -42,7 +42,7 @@
static const bool PRINT_REALIGNMENTS = false;
static const bool DEBUG_REALIGNMENT = false;
@@ -434,9 +452,9 @@ Description: Fix some spelling issues
template <typename TFragmentStore>
void addGaps(TFragmentStore & store, unsigned alignID, unsigned pos)
{
---- a/apps/fiona/error_rate_from_sam.cpp
-+++ b/apps/fiona/error_rate_from_sam.cpp
-@@ -71,7 +71,7 @@ int main(int argc, char const ** argv)
+--- seqan2.orig/apps/fiona/error_rate_from_sam.cpp
++++ seqan2/apps/fiona/error_rate_from_sam.cpp
+@@ -71,7 +71,7 @@
unsigned totalReadCount = 0; // Number of reads read.
unsigned totalErrorneousReadCount = 0; // Number of reads with errors read, excluding unaligned reads.
unsigned totalUnalignedReadCount = 0; // Number of reads without alignments.
@@ -445,9 +463,18 @@ Description: Fix some spelling issues
// Read records
---- a/apps/gustaf/msplazer_main.h
-+++ b/apps/gustaf/msplazer_main.h
-@@ -194,7 +194,7 @@ int msplazer(StellarOptions & stellarOpt
+@@ -153,7 +153,7 @@
+ std::cout << "STATISTICS\n"
+ << "total read count " << totalReadCount << "\t\t(excludes unaligned reads)\n"
+ << "unaligned read count " << totalUnalignedReadCount << "\n"
+- << "errorneous read count " << totalErrorneousReadCount << "\n"
++ << "erroneous read count " << totalErrorneousReadCount << "\n"
+ << "per read error rate " << 100.0 * totalErrorneousReadCount / totalReadCount << "\n"
+ << "\n"
+ << "total bases " << totalBaseCount << "\n"
+--- seqan2.orig/apps/gustaf/msplazer_main.h
++++ seqan2/apps/gustaf/msplazer_main.h
+@@ -194,7 +194,7 @@
++sizeCount[length(stellarMatches[i].matches)];
}
for(unsigned i = 0; i < length(sizeCount); ++ i){
@@ -456,9 +483,9 @@ Description: Fix some spelling issues
}
for(unsigned i = 0; i < length(distanceScores); ++i){
TScoreAlloc scores = distanceScores[i];
---- a/apps/seqcons2/seqcons_options.cpp
-+++ b/apps/seqcons2/seqcons_options.cpp
-@@ -122,7 +122,7 @@ void SeqConsOptions::print(std::ostream
+--- seqan2.orig/apps/seqcons2/seqcons_options.cpp
++++ seqan2/apps/seqcons2/seqcons_options.cpp
+@@ -122,7 +122,7 @@
<< "OVERLAP WINDOW SIZE \t" << overlapWindowSize << "\n"
<< "\n"
<< "K-MER SIZE \t" << kMerSize << "\n"
@@ -467,7 +494,7 @@ Description: Fix some spelling issues
<< "\n"
<< "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n"
<< "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n";
-@@ -208,7 +208,7 @@ parseCommandLine(SeqConsOptions & option
+@@ -208,7 +208,7 @@
setMinValue(parser, "k-mer-size", "5");
setDefaultValue(parser, "k-mer-size", "20");
@@ -476,9 +503,9 @@ Description: Fix some spelling issues
seqan::ArgParseOption::INTEGER, "COUNT"));
setMinValue(parser, "k-mer-max-occ", "0");
setDefaultValue(parser, "k-mer-max-occ", "200");
---- a/apps/seqcons2/seqcons_options.h
-+++ b/apps/seqcons2/seqcons_options.h
-@@ -100,7 +100,7 @@ struct SeqConsOptions
+--- seqan2.orig/apps/seqcons2/seqcons_options.h
++++ seqan2/apps/seqcons2/seqcons_options.h
+@@ -100,7 +100,7 @@
// K-mer length to use for identifying overlap candidates.
int kMerSize;
@@ -487,9 +514,9 @@ Description: Fix some spelling issues
int kMerMaxOcc;
// -----------------------------------------------------------------------
---- a/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
-+++ b/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -498,9 +525,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
-+++ b/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -509,9 +536,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.nop.sam.stderr
-+++ b/apps/seqcons2/tests/alns1.nop.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.nop.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.nop.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -520,9 +547,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.nop.txt.stderr
-+++ b/apps/seqcons2/tests/alns1.nop.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.nop.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.nop.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -531,9 +558,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
-+++ b/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -542,9 +569,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
-+++ b/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -553,9 +580,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
-+++ b/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -564,9 +591,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
-+++ b/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -575,9 +602,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.realign.sam.stderr
-+++ b/apps/seqcons2/tests/alns1.realign.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.realign.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.realign.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -586,9 +613,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/alns1.realign.txt.stderr
-+++ b/apps/seqcons2/tests/alns1.realign.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/alns1.realign.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.realign.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -597,9 +624,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/seqs1.align_consensus.stderr
-+++ b/apps/seqcons2/tests/seqs1.align_consensus.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/seqs1.align_consensus.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.align_consensus.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -608,9 +635,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/seqs1.nop.stderr
-+++ b/apps/seqcons2/tests/seqs1.nop.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/seqs1.nop.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.nop.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -619,9 +646,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
-+++ b/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -630,9 +657,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
-+++ b/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -641,9 +668,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
-+++ b/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
-@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
+--- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
+@@ -16,7 +16,7 @@
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -652,9 +679,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- a/apps/stellar/README
-+++ b/apps/stellar/README
-@@ -182,7 +182,7 @@ the command line:
+--- seqan2.orig/apps/stellar/README
++++ seqan2/apps/stellar/README
+@@ -182,7 +182,7 @@
Remove overabundant query k-mers from the k-mer index. NUM must be a
value between 0 (remove all) and 1 (remove nothing, default). k-mers with
a relative abundance above NUM are removed. The relative abundance is
@@ -663,9 +690,9 @@ Description: Fix some spelling issues
k-mers in the query sequence(s). The total number of k-mers is about
the total length of the query sequence(s).
---- a/demos/tutorial/basics/strings.cpp
-+++ b/demos/tutorial/basics/strings.cpp
-@@ -22,7 +22,7 @@ int main()
+--- seqan2.orig/demos/tutorial/basics/strings.cpp
++++ seqan2/demos/tutorial/basics/strings.cpp
+@@ -22,7 +22,7 @@
}
std::cout << std::endl;
//![iterate-and-replace]
@@ -674,7 +701,7 @@ Description: Fix some spelling issues
typedef Size<TAminoAcidString>::Type TSize;
typedef String<TSize> TCounterString;
TCounterString counter;
-@@ -30,7 +30,7 @@ int main()
+@@ -30,7 +30,7 @@
resize(counter, alphSize, 0);
for (TIter it = begin(sourceSeq); it != itEnd; goNext(it))
value(counter, ordValue(value(it))) += 1;
@@ -683,8 +710,8 @@ Description: Fix some spelling issues
//![frequency-table]
typedef Iterator<TCounterString>::Type TCounterIter;
TCounterIter countIt = begin(counter);
---- a/dox/pages/suffix_array.dox
-+++ b/dox/pages/suffix_array.dox
+--- seqan2.orig/dox/pages/suffix_array.dox
++++ seqan2/dox/pages/suffix_array.dox
@@ -13,7 +13,7 @@
* "Faster Suffix Sorting", 1999), and a quicksort based algorithm.
*
@@ -694,9 +721,9 @@ Description: Fix some spelling issues
* This is only an example for @link createSuffixArray @endlink and similar functions. For an index based substring search
* better use the more generic @link Finder @endlink class (see @Demo.Index Finder@ demo).
*
---- a/include/seqan/find/find_base.h
-+++ b/include/seqan/find/find_base.h
-@@ -187,9 +187,9 @@ struct Needle<Segment<THost, TSpec> cons
+--- seqan2.orig/include/seqan/find/find_base.h
++++ seqan2/include/seqan/find/find_base.h
+@@ -187,9 +187,9 @@
* @param[in] k Desired minimal score (for approximate matching). <tt>k</tt> is a number <tt><= 0</tt>.
* Differences are deletions, insertions, and substitutions.
*
@@ -708,9 +735,9 @@ Description: Fix some spelling issues
*
* @section Examples
*
---- a/include/seqan/find/find_begin.h
-+++ b/include/seqan/find/find_begin.h
-@@ -344,7 +344,7 @@ _findBeginInit(TPattern & pattern, TNeed
+--- seqan2.orig/include/seqan/find/find_begin.h
++++ seqan2/include/seqan/find/find_begin.h
+@@ -344,7 +344,7 @@
* @param[in,out] finder The Finder object to search through.
* @param[in,out] pattern The Pattern object to search for. This must be a pattern for approximate string matching.
* @param[in] limit The score limit. The default is the limit used during the last <tt>find</tt> call, see
@@ -719,9 +746,9 @@ Description: Fix some spelling issues
*
* @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no match.
*
---- a/include/seqan/index/index_esa_algs_multi.h
-+++ b/include/seqan/index/index_esa_algs_multi.h
-@@ -486,7 +486,7 @@ namespace seqan
+--- seqan2.orig/include/seqan/index/index_esa_algs_multi.h
++++ seqan2/include/seqan/index/index_esa_algs_multi.h
+@@ -486,7 +486,7 @@
template <typename TSTree>
@@ -730,7 +757,7 @@ Description: Fix some spelling issues
public:
typedef typename Value<TSTree>::Type TValue;
-@@ -687,21 +687,21 @@ namespace seqan
+@@ -687,21 +687,21 @@
template < typename TRepeat >
@@ -758,7 +785,7 @@ Description: Fix some spelling issues
if (it._innerStep()) {
// it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
// it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
-@@ -715,23 +715,23 @@ namespace seqan
+@@ -715,23 +715,23 @@
}
template < typename TRepeat >
@@ -786,8 +813,8 @@ Description: Fix some spelling issues
typedef typename Size<TSTree>::Type Type;
};
---- a/include/seqan/index/index_fm_dox.h
-+++ b/include/seqan/index/index_fm_dox.h
+--- seqan2.orig/include/seqan/index/index_fm_dox.h
++++ seqan2/include/seqan/index/index_fm_dox.h
@@ -475,7 +475,7 @@
* @param[in] character The character.
* @param[in] pos The position (which is included in the counting).
@@ -797,9 +824,9 @@ Description: Fix some spelling issues
*/
/*!
---- a/include/seqan/statistics/statistics_base.h
-+++ b/include/seqan/statistics/statistics_base.h
-@@ -83,13 +83,13 @@ TFloat _zscore(TStringSet W, TStringSet
+--- seqan2.orig/include/seqan/statistics/statistics_base.h
++++ seqan2/include/seqan/statistics/statistics_base.h
+@@ -83,13 +83,13 @@
}
/*
@@ -817,9 +844,9 @@ Description: Fix some spelling issues
* @param[in] haystack The text strings.
* @param[in] needle The set of patterns.
* @param[in] algoTag The tag to select the online text search algorithm with.
---- a/apps/sgip/sgip.cpp
-+++ b/apps/sgip/sgip.cpp
-@@ -72,7 +72,7 @@ enum SearchingType
+--- seqan2.orig/apps/sgip/sgip.cpp
++++ seqan2/apps/sgip/sgip.cpp
+@@ -72,7 +72,7 @@
struct SgipOption
{
// I/O options.
@@ -828,16 +855,18 @@ Description: Fix some spelling issues
CharString comparFile; // name of comparisive file(second graph)
CharString outputFile; // name of result file
CharString compareFolder;
-@@ -82,7 +82,7 @@ struct SgipOption
+@@ -82,8 +82,8 @@
FileOption activeFile;
SearchingType searchingType;
CharString algorithm; // Search strategy for metric dimension,e.g. Greedy, genetic etc.
- unsigned odimension; // metric dimension of orginal graph specified by user
+- unsigned cdimension; // metric dimension of comparitive graph specified by user
+ unsigned odimension; // metric dimension of original graph specified by user
- unsigned cdimension; // metric dimension of comparitive graph specified by user
++ unsigned cdimension; // metric dimension of comparative graph specified by user
bool showHelp;
bool showVersion;
-@@ -127,7 +127,7 @@ int _sgip(TOption & options)
+ bool isoCheck; //to check whether two input graphs are isomorphic
+@@ -127,7 +127,7 @@
char const * file1, * file2;
if (!options.isoCheck)
{
@@ -846,7 +875,7 @@ Description: Fix some spelling issues
if (!_createGraph(g1, SivaLab(), file1))
return 1;
-@@ -137,7 +137,7 @@ int _sgip(TOption & options)
+@@ -137,7 +137,7 @@
}
else
{
@@ -855,7 +884,7 @@ Description: Fix some spelling issues
file2 = toCString(options.comparFile);
if (!_createGraph(g1, SivaLab(), file1))
return 1;
-@@ -169,9 +169,9 @@ void _setupParser(TParser & parser)
+@@ -169,9 +169,9 @@
{
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
@@ -867,16 +896,21 @@ Description: Fix some spelling issues
setRequired(parser, "o");
addSection(parser, "Main Options");
addOption(parser, ArgParseOption("a", "algorithm", "Algorithm used for searching metric dimension", ArgParseArgument::STRING));
-@@ -180,7 +180,7 @@ void _setupParser(TParser & parser)
+@@ -179,10 +179,10 @@
+ addOption(parser, ArgParseOption("s", "searching", "Searching algorithm used for detecting resolving set,heuristic 0 bruteforce 1.", ArgParseArgument::INTEGER));
setDefaultValue(parser, "searching", "0");
addOption(parser, ArgParseOption("i", "isomorphism", "To check whether two given graphs are isomorphic"));
- addOption(parser, ArgParseOption("c", "comparitive", "File containing comparitive graph", ArgParseArgument::INPUT_FILE,"IN"));
+- addOption(parser, ArgParseOption("c", "comparitive", "File containing comparitive graph", ArgParseArgument::INPUT_FILE,"IN"));
- addOption(parser, ArgParseOption("od", "odimension", "Specified initial dimension of orginal graph by user", ArgParseArgument::INTEGER));
++ addOption(parser, ArgParseOption("c", "comparative", "File containing comparative graph", ArgParseArgument::INPUT_FILE,"IN"));
+ addOption(parser, ArgParseOption("od", "odimension", "Specified initial dimension of original graph by user", ArgParseArgument::INTEGER));
setDefaultValue(parser, "odimension", "3");
- addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial dimension of comparitive graph by user", ArgParseArgument::INTEGER));
+- addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial dimension of comparitive graph by user", ArgParseArgument::INTEGER));
++ addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial dimension of comparative graph by user", ArgParseArgument::INTEGER));
setDefaultValue(parser, "cdimension", "3");
-@@ -212,7 +212,7 @@ ArgumentParser::ParseResult _parseOption
+ addOption(parser, ArgParseOption("ad", "directory", "test for all graphs in a specified directory", ArgParseArgument::STRING));
+ addOption(parser, ArgParseOption("v", "verbose", "control the level of output files ", ArgParseArgument::INTEGER));
+@@ -212,14 +212,14 @@
return res;
// Extract option value.
@@ -885,3 +919,238 @@ Description: Fix some spelling issues
if (isSet(parser, "i"))
{
if (!isSet(parser, "c"))
+ {
+ if (!isSet(parser, "ad"))
+ {
+- std::cerr << "sgip" << ":comparitive file has not been specified!" << std::endl;
++ std::cerr << "sgip" << ":comparative file has not been specified!" << std::endl;
+ printShortHelp(parser, std::cerr);
+ return ArgumentParser::PARSE_ERROR;
+ }
+--- seqan2.orig/apps/gustaf/msplazer_out.h
++++ seqan2/apps/gustaf/msplazer_out.h
+@@ -1125,7 +1125,7 @@
+ std::cout << "Thresholds:" << std::endl;
+ std::cout << " overlap threshold (oth) : " << options.simThresh << std::endl;
+ std::cout << " gap threshold (gth) : " << options.gapThresh << std::endl;
+- std::cout << " inital gap threshold (ith) : " << options.initGapThresh << std::endl;
++ std::cout << " initial gap threshold (ith) : " << options.initGapThresh << std::endl;
+ std::cout << "Penalties:" << std::endl;
+ std::cout << " translocation penalty (tp) : " << options.diffDBPen << std::endl;
+ std::cout << " inversion penalty (ip) : " << options.diffStrandPen << std::endl;
+--- seqan2.orig/apps/gustaf/tests/pairedEnd_st1_l30.stdout
++++ seqan2/apps/gustaf/tests/pairedEnd_st1_l30.stdout
+@@ -6,7 +6,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/reference2_st1_l30.stdout
++++ seqan2/apps/gustaf/tests/reference2_st1_l30.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/st1_l30.stdout
++++ seqan2/apps/gustaf/tests/st1_l30.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/st1_l30_gth3.stdout
++++ seqan2/apps/gustaf/tests/st1_l30_gth3.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 3
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/st1_l30_ith5.stdout
++++ seqan2/apps/gustaf/tests/st1_l30_ith5.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 5
++ initial gap threshold (ith) : 5
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/st1_l30_m.stdout
++++ seqan2/apps/gustaf/tests/st1_l30_m.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/apps/gustaf/tests/st2_l100.stdout
++++ seqan2/apps/gustaf/tests/st2_l100.stdout
+@@ -5,7 +5,7 @@
+ Thresholds:
+ overlap threshold (oth) : 0.5
+ gap threshold (gth) : 5
+- inital gap threshold (ith) : 15
++ initial gap threshold (ith) : 15
+ Penalties:
+ translocation penalty (tp) : 5
+ inversion penalty (ip) : 5
+--- seqan2.orig/manual/source/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.rst
++++ seqan2/manual/source/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.rst
+@@ -496,7 +496,7 @@
+ Complete Solution (and more explanations)
+ .. container:: foldable
+
+- Write the `main` body of the program with type definition and initalization of the used data structures.
++ Write the `main` body of the program with type definition and initialization of the used data structures.
+
+ .. includefrags:: demos/tutorial/pairwise_sequence_alignment/assignment5.cpp
+ :fragment: main
+--- seqan2.orig/apps/mason2/mason_options.cpp
++++ seqan2/apps/mason2/mason_options.cpp
+@@ -883,22 +883,22 @@
+ setDefaultValue(parser, "sanger-quality-match-end-stddev", "2");
+
+ addOption(parser, seqan::ArgParseOption("", "sanger-quality-error-start-mean",
+- "Mean PHRED quality for errorneous bases of first base in Sanger sequencing.",
++ "Mean PHRED quality for erroneous bases of first base in Sanger sequencing.",
+ seqan::ArgParseOption::DOUBLE, "QUAL"));
+ setDefaultValue(parser, "sanger-quality-error-start-mean", "30");
+
+ addOption(parser, seqan::ArgParseOption("", "sanger-quality-error-end-mean",
+- "Mean PHRED quality for errorneous bases of last base in Sanger sequencing.",
++ "Mean PHRED quality for erroneous bases of last base in Sanger sequencing.",
+ seqan::ArgParseOption::DOUBLE, "QUAL"));
+ setDefaultValue(parser, "sanger-quality-error-end-mean", "20");
+
+ addOption(parser, seqan::ArgParseOption("", "sanger-quality-error-start-stddev",
+- "Mean PHRED quality for errorneous bases of first base in Sanger sequencing.",
++ "Mean PHRED quality for erroneous bases of first base in Sanger sequencing.",
+ seqan::ArgParseOption::DOUBLE, "QUAL"));
+ setDefaultValue(parser, "sanger-quality-error-start-stddev", "2");
+
+ addOption(parser, seqan::ArgParseOption("", "sanger-quality-error-end-stddev",
+- "Mean PHRED quality for errorneous bases of last base in Sanger sequencing.",
++ "Mean PHRED quality for erroneous bases of last base in Sanger sequencing.",
+ seqan::ArgParseOption::DOUBLE, "QUAL"));
+ setDefaultValue(parser, "sanger-quality-error-end-stddev", "5");
+ }
+--- seqan2.orig/apps/razers/razers.h
++++ seqan2/apps/razers/razers.h
+@@ -225,7 +225,7 @@
+
+ if (TSpec::DUMP_VERIFICATION_TASKS)
+ {
+- open(verifications, "verfication_tasks.bin", OPEN_WRONLY|OPEN_CREATE);
++ open(verifications, "verification_tasks.bin", OPEN_WRONLY|OPEN_CREATE);
+ }
+ }
+ };
+--- seqan2.orig/apps/razers/razers_matepairs.h
++++ seqan2/apps/razers/razers_matepairs.h
+@@ -795,7 +795,7 @@
+ ::std::cerr << ::std::endl;
+ ::std::cerr << "___FILTRATION_STATS____" << ::std::endl;
+ ::std::cerr << "Filtration counter: " << options.FP + options.TP << ::std::endl;
+- ::std::cerr << "Successful verfications: " << options.TP << ::std::endl;
++ ::std::cerr << "Successful verifications: " << options.TP << ::std::endl;
+ }
+ return 0;
+ }
+--- seqan2.orig/apps/razers3/razers.h
++++ seqan2/apps/razers3/razers.h
+@@ -3101,7 +3101,7 @@
+ std::cerr << std::endl;
+ std::cerr << "___FILTRATION_STATS____" << std::endl;
+ std::cerr << "Filtration counter: " << options.countFiltration << std::endl;
+- std::cerr << "Successful verfications: " << options.countVerification << std::endl;
++ std::cerr << "Successful verifications: " << options.countVerification << std::endl;
+ }
+ return 0;
+ }
+--- seqan2.orig/apps/razers3/razers_matepairs.h
++++ seqan2/apps/razers3/razers_matepairs.h
+@@ -1156,7 +1156,7 @@
+ std::cerr << std::endl;
+ std::cerr << "___FILTRATION_STATS____" << std::endl;
+ std::cerr << "Filtration counter: " << options.countFiltration << std::endl;
+- std::cerr << "Verfication counter: " << options.countVerification << std::endl;
++ std::cerr << "Verification counter: " << options.countVerification << std::endl;
+ }
+
+ return 0;
+--- seqan2.orig/apps/razers3/razers_matepairs_parallel.h
++++ seqan2/apps/razers3/razers_matepairs_parallel.h
+@@ -1623,7 +1623,7 @@
+ std::cerr << std::endl;
+ std::cerr << "___FILTRATION_STATS____" << std::endl;
+ std::cerr << "Filtration counter: " << options.countFiltration << std::endl;
+- std::cerr << "Verfication counter: " << options.countVerification << std::endl;
++ std::cerr << "Verification counter: " << options.countVerification << std::endl;
+ }
+
+ // Restore global state.
+--- seqan2.orig/apps/razers3/razers_parallel.h
++++ seqan2/apps/razers3/razers_parallel.h
+@@ -1163,7 +1163,7 @@
+ std::cerr << std::endl;
+ std::cerr << "___FILTRATION_STATS____" << std::endl;
+ std::cerr << "Filtration counter: " << options.countFiltration << std::endl;
+- std::cerr << "Successful verfications: " << options.countVerification << std::endl;
++ std::cerr << "Successful verifications: " << options.countVerification << std::endl;
+ }
+
+ // Restore global state.
+--- seqan2.orig/apps/rep_sep/rep_sep.cpp
++++ seqan2/apps/rep_sep/rep_sep.cpp
+@@ -73,7 +73,7 @@
+ addUsageLine(parser, "[OPTION]... --assembly <input file> --output-prefix <prefix>");
+ setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
+ setDate(parser, SEQAN_DATE);
+- setShortDescription(parser, "Repeat Seperation Tool -- Copyright (c) 2009, Stephan Aiche");
++ setShortDescription(parser, "Repeat Separation Tool -- Copyright (c) 2009, Stephan Aiche");
+
+ // needed input file
+ addOption(parser, ArgParseOption("a", "assembly", "Input assembly filename.", ArgParseArgument::INPUT_FILE));
+--- seqan2.orig/include/seqan/blast/blast_tabular_in.h
++++ seqan2/include/seqan/blast/blast_tabular_in.h
+@@ -74,7 +74,7 @@
+ Possibly other lines can be written as comments.
+
+ Because 0 matches are allowed, multiple COMMENTLINES can succeed each other, the
+-criterium for seperation employed by this implementation is that an NCBI Blast
++criterium for separation employed by this implementation is that an NCBI Blast
+ COMMENTLINES always ends after the "Fields" line and NCBI Blast+ COMMENTLINES end after
+ the "number of hits"-line.
+ */
+--- seqan2.orig/apps/stellar/stellar.cpp
++++ seqan2/apps/stellar/stellar.cpp
+@@ -262,7 +262,7 @@
+
+ std::cout << "Loaded " << seqCount << " " << name << " sequence" << ((seqCount > 1) ? "s." : ".") << std::endl;
+ if (!idsUnique)
+- std::cerr << "WARNING: Non-unique " << name << " ids. Output can be ambigous.\n";
++ std::cerr << "WARNING: Non-unique " << name << " ids. Output can be ambiguous.\n";
+ return true;
+ }
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git
More information about the debian-med-commit
mailing list