This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch debian-experimental in repository seqan2.
commit 2dc4b734116abba149190b545eefe074165da933 Author: Michael R. Crusoe <michael.cru...@gmail.com> Date: Fri Jan 13 05:33:08 2017 -0800 new upstream release --- debian/changelog | 5 +- debian/patches/series | 3 - debian/patches/spelling.patch | 1155 ----------------------------------------- debian/patches/tandem-rename | 54 -- debian/patches/typo-fix | 22 - 5 files changed, 3 insertions(+), 1236 deletions(-) diff --git a/debian/changelog b/debian/changelog index f572649..1f4e786 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,10 @@ -seqan2 (2.3.0~1.20161019~af07bc1+dfsg-5) UNRELEASED; urgency=medium +seqan2 (2.3.1+dfsg-1) experimental; urgency=medium * Try to save more memory on kfreebsd-* * Fix parallel build disabling to not produce warnings + * New upstream release, three incorporated patched removed - -- Michael R. Crusoe <michael.cru...@gmail.com> Wed, 26 Oct 2016 05:51:51 -0700 + -- Michael R. Crusoe <michael.cru...@gmail.com> Fri, 13 Jan 2017 05:36:28 -0800 seqan2 (2.3.0~1.20161019~af07bc1+dfsg-4) experimental; urgency=medium diff --git a/debian/patches/series b/debian/patches/series index 94e4c15..fe8c345 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,2 @@ -tandem-rename -typo-fix -spelling.patch short-description diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch deleted file mode 100644 index c500480..0000000 --- a/debian/patches/spelling.patch +++ /dev/null @@ -1,1155 +0,0 @@ -From: Michael R. Crusoe <michael.cru...@gmail.com> -Subject: Fix some spelling issues -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; - -- // Consider only reads that have a unique match in the mapping result file. Usefull for precision computation. -+ // Consider only reads that have a unique match in the mapping result file. Useful for precision computation. - bool onlyUniqueReads; - - // The benchmark category, one of {"all", "any-best", "all-best"}. -@@ -142,7 +142,7 @@ - // Print the missed intervals to stderr for debugging purposes. - bool showMissedIntervals; - -- // Print superflous intervals (intervals found in BAM file but have too bad score). -+ // Print superfluous intervals (intervals found in BAM file but have too bad score). - bool showSuperflousIntervals; - - // Print additional intervals (intervals found in BAM with good score that are not in WIT file). -@@ -1093,7 +1093,7 @@ - "sample position. For simulated data.")); - addOption(parser, seqan::ArgParseOption("", "only-unique-reads", - "Consider only reads that a single alignment in the mapping result file. " -- "Usefull for precision computation.")); -+ "Useful for precision computation.")); - addOption(parser, seqan::ArgParseOption("", "match-N", "When set, N matches all characters without penalty.")); - addOption(parser, seqan::ArgParseOption("", "distance-metric", - "Set distance metric. Valid values: hamming, edit. Default: edit.", -@@ -1278,7 +1278,7 @@ - << " additional " << yesNo(options.showAdditionalIntervals) << '\n' - << " hit " << yesNo(options.showHitIntervals) << '\n' - << " missed " << yesNo(options.showMissedIntervals) << '\n' -- << " superflous " << yesNo(options.showSuperflousIntervals) << '\n' -+ << " superfluous " << yesNo(options.showSuperflousIntervals) << '\n' - << " try hit " << yesNo(options.showTryHitIntervals) << '\n' - << "\n"; - -@@ -1430,7 +1430,7 @@ - if (!empty(options.outTsvPath)) - { - std::cerr << '\n' -- << "Writting output TSV " << options.outTsvPath << " ..."; -+ << "Writing output TSV " << options.outTsvPath << " ..."; - std::ofstream tsvOut(toCString(options.outTsvPath), std::ios::out | std::ios::binary); - bool failed = false; - if (!tsvOut.good()) ---- 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"); -- addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply compaction treshold by this value after reaching and compacting.", ArgParseOption::DOUBLE)); -+ addOption(parser, ArgParseOption("cm", "compact-mult", "Multiply compaction threshold by this value after reaching and compacting.", ArgParseOption::DOUBLE)); - setMinValue(parser, "compact-mult", "0"); - setDefaultValue(parser, "compact-mult", options.compactMult); - addOption(parser, ArgParseOption("ncf", "no-compact-frac", "Don't compact if in this last fraction of genome.", ArgParseOption::DOUBLE)); ---- 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 -- file name is ommitted the result is written to standard output in SAM format. -+ file name is omitted the result is written to standard output in SAM format. - - (c) Copyright 2014 by David Weese. - ---- 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. " -- "If the output file name is ommitted the result is written to stdout."); -+ "If the output file name is omitted the result is written to stdout."); - - addDescription(parser, "(c) Copyright in 2014 by David Weese."); - ---- 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) - { -- std::cerr << "An error occured. Bailing out.\n"; -+ std::cerr << "An error occurred. Bailing out.\n"; - return 1; - } - ---- seqan2.orig/apps/fiona/fiona.cpp -+++ seqan2/apps/fiona/fiona.cpp -@@ -2609,20 +2609,20 @@ - double median = 0.0; - double mediumTotalOccs = 0.0; - -- std::map<unsigned, unsigned> vectorOccurences; -+ std::map<unsigned, unsigned> vectorOccurrences; - - goBegin(iter); - for (; !atEnd(iter); ++iter) - { - unsigned numOccs = countOccurrences(iter); -- ++vectorOccurences[numOccs]; -+ ++vectorOccurrences[numOccs]; - totalOccs += numOccs; - } - - mediumTotalOccs = totalOccs / 2.0; - - std::map<unsigned,unsigned>::iterator iterMap; -- for (iterMap = vectorOccurences.begin (); iterMap != vectorOccurences.end (); ++iterMap) -+ for (iterMap = vectorOccurrences.begin (); iterMap != vectorOccurrences.end (); ++iterMap) - { - sumMedian += iterMap->second*iterMap->first; - if (sumMedian >= mediumTotalOccs) -@@ -4199,7 +4199,7 @@ - String<double> sd; - standardDeviation(sd, store.readSeqStore, options.genomeLength); - -- /*The strictness value allows to estimate the confidence intervall*/ -+ /*The strictness value allows one to estimate the confidence intervall*/ - for (unsigned i = 0; i < length(options.expectedTheoretical); ++i) - { - double expectedTemporary = options.expectedTheoretical[i] - options.strictness * sd[i]; -@@ -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 - ------------------------------------------------------------------------------ - --Mason Splicing allows to construct transcripts from a GFF/GTF file, a -+Mason Splicing allows one to construct transcripts from a GFF/GTF file, a - reference sequence and an optional variant file. - - ------------------------------------------------------------------------------ ---- seqan2.orig/apps/ngs_roi/project_spliced.h -+++ seqan2/apps/ngs_roi/project_spliced.h -@@ -31,7 +31,7 @@ - // ========================================================================== - // Author: Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de> - // ========================================================================== --// The ProjectSplicedRoi class allows to do the projection of ROIs to grouped -+// The ProjectSplicedRoi class allows one to do the projection of ROIs to grouped - // GTF/GFF intervals. - // - // This mode is enabled when the --gff-group-by KEY option is used. In this ---- 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, -- "The program allows to align two sequences using dyamic programming alignment algorithms while " -+ "The program allows one to align two sequences using dyamic programming alignment algorithms while " - "tweaking various parameters."); - - addSection(parser, "Main Options"); ---- 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 --an error occured while building the gold standard or in the evaluation -+an error occurred while building the gold standard or in the evaluation - 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 @@ - Contact - ------ - -- Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de> -\ No newline at end of file -+ Manuel Holtgrewe <manuel.holtgr...@fu-berlin.de> ---- 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, -- "This program allows to build a RABEMA gold standard. The input is a reference FASTA file " -+ "This program allows one to build a RABEMA gold standard. The input is a reference FASTA file " - "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 " ---- 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. - // --// The function rebuildMapping() allows to rebuild the mapping from two -+// The function rebuildMapping() allows one to rebuild the mapping from two - // name store caches. - // ========================================================================== - ---- 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! - --This tool allows to cut sequences and parts of sequences out of sequence -+This tool allows one to cut sequences and parts of sequences out of sequence - files. It supports all formats supported by the AutoSeqFormat class from - SeqAn, including FASTA, FASTQ and QSeq (Illumina format). - ---- seqan2.orig/apps/seqcons2/seqcons.cpp -+++ seqan2/apps/seqcons2/seqcons.cpp -@@ -92,7 +92,7 @@ - } - catch (std::runtime_error & e) - { -- std::cerr << "\nERROR: An error occured during the program's execution:\n" -+ std::cerr << "\nERROR: An error occurred during the program's execution:\n" - << " " << e.what() << "\n"; - return 1; - } ---- 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> -- <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows to store gaps independent of the underlying sequence</td></tr> -+ <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows one to store gaps independent of the underlying sequence</td></tr> - </table> - </li> - <li> ---- 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 - --<strong>Typedefs are a common, standardized C++ language feature that allows to give custom names to arbitrary types.</strong> -+<strong>Typedefs are a common, standardized C++ language feature that allows one to give custom names to arbitrary types.</strong> - - 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>. - ---- 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. - * -- * Gaps wrap a @link ContainerConcept Sequence @endlink and allows to (1) insert gaps into the sequence and (2) select -+ * Gaps wrap a @link ContainerConcept Sequence @endlink and allows one to (1) insert gaps into the sequence and (2) select - * 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. ---- seqan2.orig/include/seqan/arg_parse/tool_doc.h -+++ seqan2/include/seqan/arg_parse/tool_doc.h -@@ -568,7 +568,7 @@ - * - * @section Remarks - * -- * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows to store -+ * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows one to store - * 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. - * ---- 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. -- * It allows to operate on a single iterator, if multiple containers need to be traversed simultaneously. -+ * It allows one to operate on a single iterator, if multiple containers need to be traversed simultaneously. - * 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. ---- 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. - * -- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a -+ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a - * 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 @@ - * @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. - * -- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a -+ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a - * 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 @@ - * 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. - * -- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a -+ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a - * 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 @@ - * 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. - * -- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a -+ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a - * 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. ---- 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 -- struct MultiMemOccurences; // i.e. maximal match over different sequences -+ struct MultiMemOccurrences; // i.e. maximal match over different sequences - - - /*! -@@ -197,7 +197,7 @@ - template <typename TSize> - struct VertexEsa { - Pair<TSize> range; // current SA interval of hits (unique node identifier) -- TSize parentRight; // right boundary of parent node's range (allows to go right) -+ TSize parentRight; // right boundary of parent node's range (allows one to go right) - - - VertexEsa() : range(0, 0), parentRight(0) {} ---- 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; - -- TStack history; // contains all previously visited intervals (allows to go up) -+ TStack history; // contains all previously visited intervals (allows one to go up) - - //____________________________________________________________________________ - ---- 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 -- TSize parentRight; // right boundary of parent node's range (allows to go right) -+ TSize parentRight; // right boundary of parent node's range (allows one to go right) - - VertexWotdModified_() : - node(0), ---- 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 -- * other containers the Splitter allows to access one more element than its length would imply to allow to retrieve the -+ * other containers the Splitter allows one to access one more element than its length would imply to allow to retrieve the - * right boundary of each subinterval (see example code below). - * - * @section Examples ---- 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>. - * -- * This function allows to increase the capacity but not the length of a container. -+ * This function allows one to increase the capacity but not the length of a container. - * - * Use @link StringConcept#resize @endlink if you want to change the size of a container. - * ---- 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. - * -- * Second, the @link DependentStringSet @endlink specialization allows to create subsets of string sets without -+ * Second, the @link DependentStringSet @endlink specialization allows one to create subsets of string sets without - * storing copies of strings and identifying strings by a common id. - * - * @section Examples ---- 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. - // --// A Tabix index (Heng Li) allows to randomly seek in a tab-seperated genome -+// A Tabix index (Heng Li) allows one to randomly seek in a tab-seperated genome - // 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'. ---- seqan2.orig/manual/attic/Tutorial/IndicesOld.rst -+++ seqan2/manual/attic/Tutorial/IndicesOld.rst -@@ -3,7 +3,7 @@ - Indices - ------- - --A substring index is a datatype which allows to seek efficiently for all -+A substring index is a datatype which allows one to seek efficiently for all - 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 ---- 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 --// allocators. It allows to count the number of allocations and deallocations -+// allocators. It allows one to count the number of allocations and deallocations - // and checks whether all allocated memory blocks are correctly deallocated - // when it is destructed. - ---- 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; - --// Helper function that allows to add gaps into the i-th read alignment in a fragmentStore. -+// Helper function that allows one to add gaps into the i-th read alignment in a fragmentStore. - template <typename TFragmentStore> - void addGaps(TFragmentStore & store, unsigned alignID, unsigned pos) - { ---- 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. -- std::map<unsigned, unsigned> histo; // Histogram error count -> num occurences. -+ std::map<unsigned, unsigned> histo; // Histogram error count -> num occurrences. - - // Read records - -@@ -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){ -- std::cout << "Number of occurences for matches " << i << " : " << sizeCount[i] << std::endl; -+ std::cout << "Number of occurrences for matches " << i << " : " << sizeCount[i] << std::endl; - } - for(unsigned i = 0; i < length(distanceScores); ++i){ - TScoreAlloc scores = distanceScores[i]; ---- 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" -- << "K-MER MAX OCCURENCES \t" << kMerMaxOcc << "\n" -+ << "K-MER MAX OCCURRENCES \t" << kMerMaxOcc << "\n" - << "\n" - << "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n" - << "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n"; -@@ -208,7 +208,7 @@ - setMinValue(parser, "k-mer-size", "5"); - setDefaultValue(parser, "k-mer-size", "20"); - -- addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore k-mer with higher occurence count, 0 to disable.", -+ addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore k-mer with higher occurrence count, 0 to disable.", - seqan::ArgParseOption::INTEGER, "COUNT")); - setMinValue(parser, "k-mer-max-occ", "0"); - setDefaultValue(parser, "k-mer-max-occ", "200"); ---- 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; -- // K-mers with a higher number of occurences are ignored. -+ // K-mers with a higher number of occurrences are ignored. - int kMerMaxOcc; - - // ----------------------------------------------------------------------- ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 --K-MER MAX OCCURENCES 200 -+K-MER MAX OCCURRENCES 200 - - REALIGNMENT BANDWIDTH 10 - REALIGNMENT ENVIRONMENT 20 ---- 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 -- the absolute number of a k-mers occurences divided by the total number of -+ the absolute number of a k-mers occurrences divided by the total number of - k-mers in the query sequence(s). The total number of k-mers is about - the total length of the query sequence(s). - ---- seqan2.orig/demos/tutorial/basics/strings.cpp -+++ seqan2/demos/tutorial/basics/strings.cpp -@@ -22,7 +22,7 @@ - } - std::cout << std::endl; - //![iterate-and-replace] --//![count-occurences] -+//![count-occurrences] - typedef Size<TAminoAcidString>::Type TSize; - typedef String<TSize> TCounterString; - TCounterString counter; -@@ -30,7 +30,7 @@ - resize(counter, alphSize, 0); - for (TIter it = begin(sourceSeq); it != itEnd; goNext(it)) - value(counter, ordValue(value(it))) += 1; --//![count-occurences] -+//![count-occurrences] - //![frequency-table] - typedef Iterator<TCounterString>::Type TCounterIter; - TCounterIter countIt = begin(counter); ---- 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. - * - * The following example constructs a suffix array using the modified Skew algorithm and searches the interval of suffices -- * beginning with $t="l"$. The start positions of these suffices are the occurences of $t$, which are outputted at last. -+ * beginning with $t="l"$. The start positions of these suffices are the occurrences of $t$, which are outputted at last. - * 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). - * ---- 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. - * -- * @return bool <tt>true</tt> if an occurence was found and <tt>false</tt> if not. -+ * @return bool <tt>true</tt> if an occurrence was found and <tt>false</tt> if not. - * -- * Repeated calls of this function iterate through all occurences of <tt>pattern</tt>. -+ * Repeated calls of this function iterate through all occurrences of <tt>pattern</tt>. - * - * @section Examples - * ---- 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 -- * <tt>getScore</tt>. All occurences that score at least <tt>limit</tt> are reported. -+ * <tt>getScore</tt>. All occurrences that score at least <tt>limit</tt> are reported. - * - * @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no match. - * ---- 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> -- class Iter< MultiMem<TSTree>, MultiMemOccurences > { -+ class Iter< MultiMem<TSTree>, MultiMemOccurrences > { - public: - - typedef typename Value<TSTree>::Type TValue; -@@ -687,21 +687,21 @@ - - - template < typename TRepeat > -- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type & -- value(Iter<TRepeat, MultiMemOccurences> const &it) { -+ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type & -+ value(Iter<TRepeat, MultiMemOccurrences> const &it) { - return it.tmp; - } - - template < typename TRepeat > -- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type & -- value(Iter<TRepeat, MultiMemOccurences> &it) { -+ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type & -+ value(Iter<TRepeat, MultiMemOccurrences> &it) { - return it.tmp; - } - - //TODO:fix me - template < typename TRepeat > -- inline Iter<TRepeat, MultiMemOccurences> & -- goNext(Iter<TRepeat, MultiMemOccurences> &it) { -+ inline Iter<TRepeat, MultiMemOccurrences> & -+ goNext(Iter<TRepeat, MultiMemOccurrences> &it) { - 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 @@ - } - - template < typename TRepeat > -- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> const &it) { -+ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> const &it) { - return it._atEnd; - } - - template < typename TRepeat > -- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> &it) { -+ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> &it) { - return it._atEnd; - } - - - template <typename TSTree> - struct Iterator< MultiMem<TSTree> > { -- typedef Iter<MultiMem<TSTree>, MultiMemOccurences> Type; -+ typedef Iter<MultiMem<TSTree>, MultiMemOccurrences> Type; - }; - - template <typename TSTree> -- struct Size< Iter<MultiMem<TSTree>, MultiMemOccurences> > { -+ struct Size< Iter<MultiMem<TSTree>, MultiMemOccurrences> > { - typedef typename Size<TSTree>::Type Type; - }; - ---- 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). - * -- * @return TSize The number of occurences (Metafunction: @link Index#Size @endlink). -+ * @return TSize The number of occurrences (Metafunction: @link Index#Size @endlink). - */ - - /*! ---- seqan2.orig/include/seqan/statistics/statistics_base.h -+++ seqan2/include/seqan/statistics/statistics_base.h -@@ -83,13 +83,13 @@ - } - - /* -- * @fn _numOccurences -+ * @fn _numOccurrences - * @headerfile <seqan/statistics.h> -- * @brief Auxiliary function to compute the number of occurences of a set of patterns in a set of text strings. -+ * @brief Auxiliary function to compute the number of occurrences of a set of patterns in a set of text strings. - * -- * @signature void _numOccurences(W, haystack, needle, algoTag); -+ * @signature void _numOccurrences(W, haystack, needle, algoTag); - * -- * @param[in,out] W A counter, incremented by the number of occurences. -+ * @param[in,out] W A counter, incremented by the number of occurrences. - * @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. ---- seqan2.orig/apps/sgip/sgip.cpp -+++ seqan2/apps/sgip/sgip.cpp -@@ -72,7 +72,7 @@ - struct SgipOption - { - // I/O options. -- CharString orginalFile; // name of orginal file(first graph) -+ CharString originalFile; // name of original file(first graph) - CharString comparFile; // name of comparisive file(second graph) - CharString outputFile; // name of result file - CharString compareFolder; -@@ -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 comparative graph specified by user - bool showHelp; - bool showVersion; - bool isoCheck; //to check whether two input graphs are isomorphic -@@ -127,7 +127,7 @@ - char const * file1, * file2; - if (!options.isoCheck) - { -- file1 = toCString(options.orginalFile); -+ file1 = toCString(options.originalFile); - if (!_createGraph(g1, SivaLab(), file1)) - return 1; - -@@ -137,7 +137,7 @@ - } - else - { -- file1 = toCString(options.orginalFile); -+ file1 = toCString(options.originalFile); - file2 = toCString(options.comparFile); - if (!_createGraph(g1, SivaLab(), file1)) - return 1; -@@ -169,9 +169,9 @@ - { - setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]"); - addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem"); -- addUsageLine(parser, "-o <orginal graph> [Option]"); -+ addUsageLine(parser, "-o <original graph> [Option]"); - addSection(parser, "Mandatory Options"); -- addOption(parser, ArgParseOption("o", "orginal", "File containing orginal graph", ArgParseArgument::INPUT_FILE,"IN")); -+ addOption(parser, ArgParseOption("o", "original", "File containing original graph", ArgParseArgument::INPUT_FILE,"IN")); - setRequired(parser, "o"); - addSection(parser, "Main Options"); - addOption(parser, ArgParseOption("a", "algorithm", "Algorithm used for searching metric dimension", ArgParseArgument::STRING)); -@@ -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("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 comparative graph by user", ArgParseArgument::INTEGER)); - setDefaultValue(parser, "cdimension", "3"); - 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. -- getOptionValue(options.orginalFile, parser, "o"); -+ getOptionValue(options.originalFile, parser, "o"); - 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; - } - diff --git a/debian/patches/tandem-rename b/debian/patches/tandem-rename deleted file mode 100644 index 50e626c..0000000 --- a/debian/patches/tandem-rename +++ /dev/null @@ -1,54 +0,0 @@ -From: Michael R. Crusoe <michael.cru...@gmail.com> -Subject: Work around GNU Hurd's TANDEM constant -https://fossies.org/dox/glibc-2.24/sysdeps_2mach_2hurd_2bits_2ioctls_8h.html#aea2b0b2a11b94d258198cd2104bc79a4 ---- seqan2.orig/apps/gustaf/msplazer.h -+++ seqan2/apps/gustaf/msplazer.h -@@ -134,7 +134,7 @@ - INSERTION, // 1 - DELETION, // 2 - INVERSION, // 3 -- TANDEM, // 4 -+ SEQAN_TANDEM, // 4 TANDEM is an IOCTL numeric constant in Hurd - DISPDUPLICATION, // 5 - INTERTRANSLOCATION, // 6 - TRANSLOCATION, // 7 -@@ -696,7 +696,7 @@ - case TBreakpoint::INVERSION: - out << "SVType: inversion"; - break; -- case TBreakpoint::TANDEM: -+ case TBreakpoint::SEQAN_TANDEM: - out << "SVType: tandem"; - break; - case TBreakpoint::DISPDUPLICATION: ---- seqan2.orig/apps/gustaf/msplazer_algorithms.h -+++ seqan2/apps/gustaf/msplazer_algorithms.h -@@ -493,7 +493,7 @@ - // Double overlap check (not handled jet) - // std::cerr << "double overlap in reference and read called from read overlap" << std::endl; - // std::cout << "Translocation double overlap" << std::endl; -- bp.svtype = TBreakpoint::TANDEM; -+ bp.svtype = TBreakpoint::SEQAN_TANDEM; - } - - //std::cout << "Breakpoint " << bp << std::endl; ---- seqan2.orig/apps/gustaf/msplazer_out.h -+++ seqan2/apps/gustaf/msplazer_out.h -@@ -196,7 +196,7 @@ - case TBreakpoint::INVERSION: - record.type = "inversion"; - break; -- case TBreakpoint::TANDEM: -+ case TBreakpoint::SEQAN_TANDEM: - record.type = "tandem"; - break; - case TBreakpoint::DISPDUPLICATION: -@@ -647,7 +647,7 @@ - case TBreakpoint::INVERSION: - _fillVcfRecordInversion(record, bp, ref, id); - return 1; -- case TBreakpoint::TANDEM: -+ case TBreakpoint::SEQAN_TANDEM: - _fillVcfRecordTandem(record, bp, ref, id); - return 1; - case TBreakpoint::DISPDUPLICATION: diff --git a/debian/patches/typo-fix b/debian/patches/typo-fix deleted file mode 100644 index 2d8ff2d..0000000 --- a/debian/patches/typo-fix +++ /dev/null @@ -1,22 +0,0 @@ -From: Michael R. Crusoe <michael.cru...@gail.com -Subject: Fix typo ---- seqan2.orig/include/seqan/parallel/parallel_lock.h -+++ seqan2/include/seqan/parallel/parallel_lock.h -@@ -218,14 +218,14 @@ - #elif defined(__arm__) || defined(__aarch64__) // ARM. - __asm__ __volatile__ ("yield" ::: "memory"); - #elif defined(__sparc) || defined(__sparc__) // SPARC --#if definde(__SUNPRO_C) -+#if defined(__SUNPRO_C) - __asm __volatile__ ("rd %%ccr, %%g0\n\t" - "rd %%ccr, %%g0\n\t" -- "rd %%ccr, %%g0") -+ "rd %%ccr, %%g0"); - #else - __asm __volatile__ ("rd %ccr, %g0\n\t" - "rd %ccr, %g0\n\t" -- "rd %ccr, %g0") -+ "rd %ccr, %g0"); - #endif // defined(__SUNPRO_C) - #elif defined(__ppc__) || defined(__ppc64__) || defined(_ARCH_PPC) || defined(_ARCH_PPC64) // PowerPC - __asm__ __volatile__ ("or 27,27,27" ::: "memory"); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit