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commit 1c4890645d271c51a636f6b4989c7783b87d23a0 Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> 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 <[email protected]> @@ -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 <[email protected]> \ No newline at end of file + Manuel Holtgrewe <[email protected]> ---- 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
