[med-svn] [seqan2] 04/04: Adapt patch
Andreas Tille
tille at debian.org
Wed Aug 3 20:18:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqan2.
commit 77c243228d1006d91c3b554d475ea383a4f029a6
Author: Andreas Tille <tille at debian.org>
Date: Wed Aug 3 21:29:28 2016 +0200
Adapt patch
---
debian/patches/spelling.patch | 554 +++++++++++++++---------------------------
1 file changed, 197 insertions(+), 357 deletions(-)
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 506e421..63f5e0f 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 18 Jan 2016 15:00:43 +0100
Description: Fix some spelling issues
---- seqan2.orig/apps/rabema/rabema_evaluate.cpp
-+++ seqan2/apps/rabema/rabema_evaluate.cpp
-@@ -91,7 +91,7 @@
+--- a/apps/rabema/rabema_evaluate.cpp
++++ b/apps/rabema/rabema_evaluate.cpp
+@@ -91,7 +91,7 @@ public:
// 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 @@
+@@ -142,7 +142,7 @@ public:
// 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 @@
+@@ -1093,7 +1093,7 @@ parseCommandLine(RabemaEvaluationOptions
"sample position. For simulated data."));
addOption(parser, seqan::ArgParseOption("", "only-unique-reads",
"Consider only reads that a single alignment in the mapping result file. "
@@ -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 @@
+@@ -1278,7 +1278,7 @@ int main(int argc, char const ** argv)
<< " additional " << yesNo(options.showAdditionalIntervals) << '\n'
<< " hit " << yesNo(options.showHitIntervals) << '\n'
<< " missed " << yesNo(options.showMissedIntervals) << '\n'
@@ -40,7 +40,7 @@ Description: Fix some spelling issues
<< " try hit " << yesNo(options.showTryHitIntervals) << '\n'
<< "\n";
-@@ -1430,7 +1430,7 @@
+@@ -1430,7 +1430,7 @@ int main(int argc, char const ** argv)
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())
---- seqan2.orig/util/py_lib/seqan/dox/validation.py
-+++ seqan2/util/py_lib/seqan/dox/validation.py
-@@ -97,7 +97,7 @@
+--- a/util/py_lib/seqan/dox/validation.py
++++ b/util/py_lib/seqan/dox/validation.py
+@@ -97,7 +97,7 @@ class ReturnVoidValidator(ProcDocValidat
return # Skip if type has no returns member.
for r in proc_entry.returns:
if r.type == 'void':
@@ -60,9 +60,9 @@ Description: Fix some spelling issues
self.msg_printer.printTokenError(r.raw.first_token, msg, 'warning')
---- seqan2.orig/apps/razers3/razers.cpp
-+++ seqan2/apps/razers3/razers.cpp
-@@ -437,7 +437,7 @@
+--- a/apps/razers3/razers.cpp
++++ b/apps/razers3/razers.cpp
+@@ -437,7 +437,7 @@ void setUpArgumentParser(ArgumentParser
addOption(parser, ArgParseOption("mf", "mismatch-file", "Write mismatch patterns to \\fIFILE\\fP.", ArgParseOption::STRING, "FILE"));
addSection(parser, "Misc Options");
@@ -71,9 +71,9 @@ 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));
---- seqan2.orig/apps/samcat/README
-+++ seqan2/apps/samcat/README
-@@ -6,7 +6,7 @@
+--- a/apps/samcat/README
++++ b/apps/samcat/README
+@@ -6,7 +6,7 @@ SYNOPSIS
DESCRIPTION
This tool reads a set of input files in SAM or BAM format and outputs the concatenation of them. If the output
@@ -82,9 +82,9 @@ Description: Fix some spelling issues
(c) Copyright 2014 by David Weese.
---- seqan2.orig/apps/samcat/samcat.cpp
-+++ seqan2/apps/samcat/samcat.cpp
-@@ -174,7 +174,7 @@
+--- a/apps/samcat/samcat.cpp
++++ b/apps/samcat/samcat.cpp
+@@ -174,7 +174,7 @@ parseCommandLine(AppOptions & options, i
addDescription(parser, "This tool reads a set of input files in SAM format "
#endif
"and outputs the concatenation of them. "
@@ -93,9 +93,9 @@ Description: Fix some spelling issues
addDescription(parser, "(c) Copyright in 2014 by David Weese.");
---- seqan2.orig/apps/fiona/compute_gain.cpp
-+++ seqan2/apps/fiona/compute_gain.cpp
-@@ -1124,7 +1124,7 @@
+--- a/apps/fiona/compute_gain.cpp
++++ b/apps/fiona/compute_gain.cpp
+@@ -1124,7 +1124,7 @@ int main(int argc, char const ** argv)
std::cerr << "WARNING: Files not read completely!\n";
if (error)
{
@@ -104,9 +104,9 @@ Description: Fix some spelling issues
return 1;
}
---- seqan2.orig/apps/fiona/fiona.cpp
-+++ seqan2/apps/fiona/fiona.cpp
-@@ -2603,20 +2603,20 @@
+--- a/apps/fiona/fiona.cpp
++++ b/apps/fiona/fiona.cpp
+@@ -2609,20 +2609,20 @@ double medianLevel(Iter<TIndex, VSTree<T
double median = 0.0;
double mediumTotalOccs = 0.0;
@@ -130,7 +130,7 @@ Description: Fix some spelling issues
{
sumMedian += iterMap->second*iterMap->first;
if (sumMedian >= mediumTotalOccs)
-@@ -4193,7 +4193,7 @@
+@@ -4199,7 +4199,7 @@ unsigned correctReads(
String<double> sd;
standardDeviation(sd, store.readSeqStore, options.genomeLength);
@@ -139,9 +139,9 @@ Description: Fix some spelling issues
for (unsigned i = 0; i < length(options.expectedTheoretical); ++i)
{
double expectedTemporary = options.expectedTheoretical[i] - options.strictness * sd[i];
---- seqan2.orig/apps/mason2/README.mason_splicing
-+++ seqan2/apps/mason2/README.mason_splicing
-@@ -19,7 +19,7 @@
+--- a/apps/mason2/README.mason_splicing
++++ b/apps/mason2/README.mason_splicing
+@@ -19,7 +19,7 @@ Table of Contents
1. Overview
------------------------------------------------------------------------------
@@ -150,8 +150,8 @@ Description: Fix some spelling issues
reference sequence and an optional variant file.
------------------------------------------------------------------------------
---- seqan2.orig/apps/ngs_roi/project_spliced.h
-+++ seqan2/apps/ngs_roi/project_spliced.h
+--- a/apps/ngs_roi/project_spliced.h
++++ b/apps/ngs_roi/project_spliced.h
@@ -31,7 +31,7 @@
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
@@ -161,9 +161,9 @@ Description: Fix some spelling issues
// 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 @@
+--- a/apps/pair_align/pair_align.cpp
++++ b/apps/pair_align/pair_align.cpp
+@@ -33,7 +33,7 @@ parseCommandLine(Options & options, int
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-s\\fP \\fIIN\\fP");
setCategory(parser, "Sequence Alignment");
addDescription(parser,
@@ -172,9 +172,9 @@ Description: Fix some spelling issues
"tweaking various parameters.");
addSection(parser, "Main Options");
---- seqan2.orig/apps/rabema/README
-+++ seqan2/apps/rabema/README
-@@ -112,7 +112,7 @@
+--- a/apps/rabema/README
++++ b/apps/rabema/README
+@@ -112,7 +112,7 @@ passed an error rate of 8% to the evalua
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
@@ -183,16 +183,16 @@ 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 @@
+@@ -136,4 +136,4 @@ reports generated by Rabema.
Contact
------
- Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
\ No newline at end of file
+ Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
---- seqan2.orig/apps/rabema/rabema_build_gold_standard.cpp
-+++ seqan2/apps/rabema/rabema_build_gold_standard.cpp
-@@ -986,7 +986,7 @@
+--- a/apps/rabema/rabema_build_gold_standard.cpp
++++ b/apps/rabema/rabema_build_gold_standard.cpp
+@@ -986,7 +986,7 @@ parseCommandLine(BuildGoldStandardOption
"[\\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,
@@ -201,8 +201,8 @@ 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 "
---- seqan2.orig/apps/rabema/ref_id_mapping.h
-+++ seqan2/apps/rabema/ref_id_mapping.h
+--- a/apps/rabema/ref_id_mapping.h
++++ b/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.
@@ -212,8 +212,8 @@ Description: Fix some spelling issues
// name store caches.
// ==========================================================================
---- seqan2.orig/apps/sak/README
-+++ seqan2/apps/sak/README
+--- a/apps/sak/README
++++ b/apps/sak/README
@@ -1,6 +1,6 @@
Swiss Army Knife tool... It slices and dices and makes the laundry!
@@ -222,9 +222,9 @@ Description: Fix some spelling issues
files. It supports all formats supported by the AutoSeqFormat class from
SeqAn, including FASTA, FASTQ and QSeq (Illumina format).
---- seqan2.orig/apps/seqcons2/seqcons.cpp
-+++ seqan2/apps/seqcons2/seqcons.cpp
-@@ -92,7 +92,7 @@
+--- a/apps/seqcons2/seqcons.cpp
++++ b/apps/seqcons2/seqcons.cpp
+@@ -92,7 +92,7 @@ int main(int argc, char const ** argv)
}
catch (std::runtime_error & e)
{
@@ -233,9 +233,9 @@ Description: Fix some spelling issues
<< " " << e.what() << "\n";
return 1;
}
---- seqan2.orig/dox/pages/index.dox
-+++ seqan2/dox/pages/index.dox
-@@ -53,7 +53,7 @@
+--- a/dox/pages/index.dox
++++ b/dox/pages/index.dox
+@@ -40,7 +40,7 @@ Alternatively you might want to check th
<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>
@@ -244,9 +244,9 @@ Description: Fix some spelling issues
</table>
</li>
<li>
---- seqan2.orig/dox/pages/language_entities.dox
-+++ seqan2/dox/pages/language_entities.dox
-@@ -16,7 +16,7 @@
+--- a/dox/pages/language_entities.dox
++++ b/dox/pages/language_entities.dox
+@@ -16,7 +16,7 @@ We call the above mentioned things like
@htmlonly <h2 data-lang-entity="typedef" id="typedef">Typedef</h2> @endhtmlonly
@@ -255,9 +255,9 @@ 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>.
---- seqan2.orig/include/seqan/align/gaps_base.h
-+++ seqan2/include/seqan/align/gaps_base.h
-@@ -112,7 +112,7 @@
+--- a/include/seqan/align/gaps_base.h
++++ b/include/seqan/align/gaps_base.h
+@@ -112,7 +112,7 @@ typedef Tag<RightOfViewPos_> RightOfView
* @tparam TSequence The type of the underlying sequence.
* @tparam TSpec Tag for specialization.
*
@@ -266,9 +266,9 @@ 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.
---- seqan2.orig/include/seqan/arg_parse/tool_doc.h
-+++ seqan2/include/seqan/arg_parse/tool_doc.h
-@@ -568,7 +568,7 @@
+--- a/include/seqan/arg_parse/tool_doc.h
++++ b/include/seqan/arg_parse/tool_doc.h
+@@ -568,7 +568,7 @@ public:
*
* @section Remarks
*
@@ -277,9 +277,9 @@ 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.
*
---- seqan2.orig/include/seqan/basic/iterator_zip.h
-+++ seqan2/include/seqan/basic/iterator_zip.h
-@@ -82,7 +82,7 @@
+--- a/include/seqan/basic/iterator_zip.h
++++ b/include/seqan/basic/iterator_zip.h
+@@ -82,7 +82,7 @@ typedef Tag<ZipIterator_> ZipIterator;
* @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.
@@ -288,9 +288,9 @@ 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.
---- seqan2.orig/include/seqan/basic/metaprogramming_enable_if.h
-+++ seqan2/include/seqan/basic/metaprogramming_enable_if.h
-@@ -252,7 +252,7 @@
+--- a/include/seqan/basic/metaprogramming_enable_if.h
++++ b/include/seqan/basic/metaprogramming_enable_if.h
+@@ -252,7 +252,7 @@ struct DisableIf2<true, T> {};
* @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.
*
@@ -299,7 +299,7 @@ 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 @@
+@@ -280,7 +280,7 @@ struct DisableIf2<true, T> {};
* @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.
*
@@ -308,7 +308,7 @@ 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 @@
+@@ -309,7 +309,7 @@ struct DisableIf2<true, T> {};
* 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.
*
@@ -317,7 +317,7 @@ 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 @@
+@@ -338,7 +338,7 @@ struct DisableIf2<true, T> {};
* 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.
*
@@ -326,9 +326,9 @@ 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.
---- seqan2.orig/include/seqan/index/index_esa_base.h
-+++ seqan2/include/seqan/index/index_esa_base.h
-@@ -169,7 +169,7 @@
+--- a/include/seqan/index/index_esa_base.h
++++ b/include/seqan/index/index_esa_base.h
+@@ -169,7 +169,7 @@ namespace seqan
typedef MaxRepeats_<void> MaxRepeats; // maximal repeat
struct MaxRepeatOccurrences;
typedef MaxRepeats_<MultiMems_> MultiMems; // Multiple Maximal Exact Match
@@ -337,18 +337,18 @@ Description: Fix some spelling issues
/*!
-@@ -197,7 +197,7 @@
+@@ -197,7 +197,7 @@ namespace seqan
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)
- SEQAN_HOST_DEVICE
+
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 @@
+--- 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
typedef typename HistoryStack_<Iter>::Type TStack;
typedef Iter iterator;
@@ -357,9 +357,9 @@ Description: Fix some spelling issues
//____________________________________________________________________________
---- seqan2.orig/include/seqan/index/index_wotd.h
-+++ seqan2/include/seqan/index/index_wotd.h
-@@ -311,7 +311,7 @@
+--- a/include/seqan/index/index_wotd.h
++++ b/include/seqan/index/index_wotd.h
+@@ -323,7 +323,7 @@ SEQAN_CONCEPT_IMPL((Index<TText, IndexWo
TSize parentRepLen; // representative length of parent node
TSize edgeLen; // length of edge above current node
Pair<TSize> range; // current SA interval of hits
@@ -368,9 +368,9 @@ Description: Fix some spelling issues
VertexWotdModified_() :
node(0),
---- seqan2.orig/include/seqan/parallel/parallel_splitting.h
-+++ seqan2/include/seqan/parallel/parallel_splitting.h
-@@ -58,7 +58,7 @@
+--- a/include/seqan/parallel/parallel_splitting.h
++++ b/include/seqan/parallel/parallel_splitting.h
+@@ -58,7 +58,7 @@ typedef Tag<Equidistant_> Equidistant;
* 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
@@ -379,9 +379,9 @@ Description: Fix some spelling issues
* 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 @@
+--- a/include/seqan/sequence/sequence_interface.h
++++ b/include/seqan/sequence/sequence_interface.h
+@@ -1101,7 +1101,7 @@ _capacityReturned(T const &,
* @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>.
*
@@ -390,9 +390,9 @@ Description: Fix some spelling issues
*
* 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 @@
+--- a/include/seqan/sequence/string_set_base.h
++++ b/include/seqan/sequence/string_set_base.h
+@@ -69,7 +69,7 @@ struct Owner {};
* 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.
*
@@ -401,19 +401,8 @@ Description: Fix some spelling issues
* storing copies of strings and identifying strings by a common id.
*
* @section Examples
---- seqan2.orig/include/seqan/system/system_condition.h
-+++ seqan2/include/seqan/system/system_condition.h
-@@ -32,7 +32,7 @@
- // Author: David Weese <david.weese at fu-berlin.de>
- // ==========================================================================
- // Condition class. In conjunction with a critical section (given in the
--// c'tor) this class allows to suspend a thread until another wakes it up via
-+// c'tor) this class allows one to suspend a thread until another wakes it up via
- // signal().
- // ==========================================================================
-
---- seqan2.orig/include/seqan/tabix_io/tabix_index_tbi.h
-+++ seqan2/include/seqan/tabix_io/tabix_index_tbi.h
+--- a/include/seqan/tabix_io/tabix_index_tbi.h
++++ b/include/seqan/tabix_io/tabix_index_tbi.h
@@ -33,7 +33,7 @@
// ==========================================================================
// (Read-only) Tabix index support.
@@ -423,9 +412,9 @@ 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'.
---- seqan2.orig/manual/attic/Tutorial/IndicesOld.rst
-+++ seqan2/manual/attic/Tutorial/IndicesOld.rst
-@@ -3,7 +3,7 @@
+--- a/manual/attic/Tutorial/IndicesOld.rst
++++ b/manual/attic/Tutorial/IndicesOld.rst
+@@ -3,7 +3,7 @@ TOC
Indices
-------
@@ -434,136 +423,9 @@ 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
---- seqan2.orig/manual/source/HowTo/FixWhitespaceAutomatically.rst
-+++ seqan2/manual/source/HowTo/FixWhitespaceAutomatically.rst
-@@ -11,7 +11,7 @@
- This page describes how to use `Universal Indent GUI <http://universalindent.sourceforge.net/>`_ and `Uncrustify <http://uncrustify.sourceforge.net/>`_ to automatically fix whitespace such that code resembles the :ref:`style-guide-cpp` more closely.
-
- * Uncrustify is a command line program that is given a style definition and a source file and reformats the source file according to the configuration.
--* Universal Indent GUI is a graphical front-end to Uncrustify with life preview that allows to manipulate the configuration and immediately see the results.
-+* Universal Indent GUI is a graphical front-end to Uncrustify with life preview that allows one to manipulate the configuration and immediately see the results.
-
- Installing Universal Indent GUI
- -------------------------------
---- seqan2.orig/manual/source/StyleGuide/Cpp.rst
-+++ seqan2/manual/source/StyleGuide/Cpp.rst
-@@ -154,7 +154,7 @@
-
- Write const correct code.
- Read the `C++ FAQ const correctness article <http://www.parashift.com/c ++-faq-lite/const-correctness.html>`_ for more information.
--Besides other things, this allows to use temporary objects without copying in functions that do not need to change their arguments.
-+Besides other things, this allows one to use temporary objects without copying in functions that do not need to change their arguments.
-
- Compiler Warnings
- ^^^^^^^^^^^^^^^^^
---- seqan2.orig/manual/source/StyleGuide/DoxApiDocs.rst
-+++ seqan2/manual/source/StyleGuide/DoxApiDocs.rst
-@@ -879,7 +879,7 @@
- Our usability research indicates that some functionality is confusing
- (e.g. see #1050) but cannot be removed. One example is the function
- ``reserve()`` which can be used to *increase* the *capacity* of a
--container whereas the function ``resize()`` allows to change the *size*
-+container whereas the function ``resize()`` allows one to change the *size*
- of a container, *increasing or decreasing* its size.
-
- The documentation of such functions should contain a clarifying text and
---- seqan2.orig/manual/source/Tutorial/BackgroundAndMotivation.rst
-+++ seqan2/manual/source/Tutorial/BackgroundAndMotivation.rst
-@@ -68,14 +68,14 @@
- Memory Management in SeqAn
- ~~~~~~~~~~~~~~~~~~~~~~~~~~
-
--C++ allows to allocate complex objects on the stack (in contrast to Java where objects are always constructed on the heap).
-+C++ allows one to allocate complex objects on the stack (in contrast to Java where objects are always constructed on the heap).
- The objects are constructed when the code execution enters the scope/block they are defined in and freed when the block is left.
- Allocation of resources (e.g. memory) happens on construction and deallocation happens when the current block is left.
- This is best explained in an example.
-
- .. includefrags:: demos/tutorial/background_and_motivation/example.cpp
-
--``seqan::String<char>`` is a class (actually an instantiation of the class template :dox:`String`) that allows to store strings of ``char`` values, similar to ``std::vector<char>`` or ``std::string``.
-+``seqan::String<char>`` is a class (actually an instantiation of the class template :dox:`String`) that allows one to store strings of ``char`` values, similar to ``std::vector<char>`` or ``std::string``.
-
- When the variable ``programName`` is allocated, the constructor of the ``String<char>`` class is called.
- It allocates sufficient memory to store the value of ``argv[0]`` and then copies over the values from this string.
---- seqan2.orig/manual/source/Tutorial/FileIOOverview.rst
-+++ seqan2/manual/source/Tutorial/FileIOOverview.rst
-@@ -34,7 +34,7 @@
- Formatted Files
- """""""""""""""
-
--SeqAn allows to read or write record-structured files through two types of classes: :dox:`FormattedFileIn` and :dox:`FormattedFileOut`.
-+SeqAn allows one to read or write record-structured files through two types of classes: :dox:`FormattedFileIn` and :dox:`FormattedFileOut`.
- Classes of type :dox:`FormattedFileIn` allow to read files, whereas classes of type :dox:`FormattedFileOut` allow to write files.
- Note how these types of classes **do not allow to read and write the same file at the same time**.
-
-@@ -62,7 +62,7 @@
-
- This tutorial shows the basic functionalities provided by any class of type :dox:`FormattedFileIn` or :dox:`FormattedFileOut`.
- In particular, this tutorial adopts the classes :dox:`BamFileIn` and :dox:`BamFileOut` as concrete types.
--The class :dox:`BamFileIn` allows to read files in SAM or BAM format, whereas the class :dox:`BamFileOut` allows to write them.
-+The class :dox:`BamFileIn` allows one to read files in SAM or BAM format, whereas the class :dox:`BamFileOut` allows one to write them.
- Nonetheless, **these functionalities are independent from the particular file format** and thus valid for all record-based file formats supported by SeqAn.
-
- The demo application shown here is a simple BAM to SAM converter.
---- seqan2.orig/manual/source/Tutorial/GffAndGtfIO.rst
-+++ seqan2/manual/source/Tutorial/GffAndGtfIO.rst
-@@ -38,7 +38,7 @@
-
- Format Version Support in SeqAn
-
-- :dox:`GffFileIn` allows to read GFF files in version 2 and 3 and GTF files.
-+ :dox:`GffFileIn` allows one to read GFF files in version 2 and 3 and GTF files.
- For writing, :dox:`GffFileOut` supports only GFF 3 and GTF.
-
- GFF Format
---- seqan2.orig/manual/source/Tutorial/IndexedFastaIO.rst
-+++ seqan2/manual/source/Tutorial/IndexedFastaIO.rst
-@@ -27,7 +27,7 @@
- If the FASTA file is named ``path/sequence.fasta``, the index file is usually named ``path/sequence.fasta.fai``.
-
- Using such index files, it is possible to rapidly read parts of the given sequence file.
--The module ``<seqan/seq_io.h>`` allows to create and read such ``.fai`` index files and exposes an API to read parts randomly of FASTA file.
-+The module ``<seqan/seq_io.h>`` allows one to create and read such ``.fai`` index files and exposes an API to read parts randomly of FASTA file.
-
- .. note::
-
---- seqan2.orig/manual/source/Tutorial/SeedAndExtend.rst
-+++ seqan2/manual/source/Tutorial/SeedAndExtend.rst
-@@ -34,7 +34,7 @@
- :align: right
- :width: 300px
-
--The :dox:`Seed` class allows to store seeds. Seeds have a begin and end position in each sequence. Often, two or more close seeds are combined into a larger seed, possibly causing a shift in horizontal or vertical direction between the begin position of the upper left seed and the end position of the lower right seed. For this reason, the :dox:`Seed` class also stores an upper and a lower diagonal to reflect the expansion between those shifted seeds.
-+The :dox:`Seed` class allows one to store seeds. Seeds have a begin and end position in each sequence. Often, two or more close seeds are combined into a larger seed, possibly causing a shift in horizontal or vertical direction between the begin position of the upper left seed and the end position of the lower right seed. For this reason, the :dox:`Seed` class also stores an upper and a lower diagonal to reflect the expansion between those shifted seeds.
-
- The image to the right shows an example where three smaller seeds (black diagonals) were combined (or "chained locally") into one larger seed (green nine-sided area).
- The first seed lies on the begin diagonal, the lowermost seed on the lower diagonal and the uppermost seed on the upper diagonal.
---- seqan2.orig/manual/source/Tutorial/SimpleRnaSeq.rst
-+++ seqan2/manual/source/Tutorial/SimpleRnaSeq.rst
-@@ -21,7 +21,7 @@
- :ref:`tutorial-genome-annotations`, :ref:`tutorial-fragment-store`, experience with OpenMP (optional)
-
- RNA-Seq refers to high-throughput sequencing of cDNA in order to get information about the RNA molecules available in a sample.
--Knowing the sequence and abundance of mRNA allows to determine the (differential) expression of genes, to detect alternative splicing variants, or to annotate yet unknown genes.
-+Knowing the sequence and abundance of mRNA allows one to determine the (differential) expression of genes, to detect alternative splicing variants, or to annotate yet unknown genes.
-
- In the following tutorial you will develop a simple gene quantification tool.
- It will load a file containing gene annotations and a file with RNA-Seq read alignments, computes abundances, and outputs RPKM values for each expressed gene.
---- seqan2.orig/manual/source/Tutorial/VcfIO.rst
-+++ seqan2/manual/source/Tutorial/VcfIO.rst
-@@ -38,7 +38,7 @@
- For simple variants such as SNPs and small indels, each record corresponds to a variant.
- More complex variants can be stored in multiple records (see the VCF standard on "breakends" for more information).
-
--The ``vcf_io`` module of SeqAn allows to read and write VCF files record-wise.
-+The ``vcf_io`` module of SeqAn allows one to read and write VCF files record-wise.
- Since the structure of the fields in the VCF format often is very complex and the format undergoes changes in this respect, SeqAn only offers basic parsing functionality: The position is stored as a 0-based integer, reference names are stored in a reference name store (similar as in the :ref:`tutorial-sam-bam-io` Tutorial), and the quality is stored as a ``float`` value.
-
- The remaining fields have to be parsed from and composed as strings in the user's application.
---- seqan2.orig/tests/basic/test_basic_allocator.h
-+++ seqan2/tests/basic/test_basic_allocator.h
-@@ -49,7 +49,7 @@
+--- a/tests/basic/test_basic_allocator.h
++++ b/tests/basic/test_basic_allocator.h
+@@ -49,7 +49,7 @@ using namespace seqan;
// ==========================================================================
// The following helper class is passed as the parent allocator to all tested
@@ -572,8 +434,8 @@ Description: Fix some spelling issues
// 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
+--- a/tests/realign/test_realign.cpp
++++ b/tests/realign/test_realign.cpp
@@ -42,7 +42,7 @@
static const bool PRINT_REALIGNMENTS = false;
static const bool DEBUG_REALIGNMENT = false;
@@ -583,20 +445,9 @@ Description: Fix some spelling issues
template <typename TFragmentStore>
void addGaps(TFragmentStore & store, unsigned alignID, unsigned pos)
{
---- seqan2.orig/util/cmake/FindSeqAn.cmake
-+++ seqan2/util/cmake/FindSeqAn.cmake
-@@ -84,7 +84,7 @@
- # SEQAN_DEFINITIONS
- #
- # Additionally, the following two variables are set. The first contains
--# the include paths for SeqAn, the second for dependencies. This allows to
-+# the include paths for SeqAn, the second for dependencies. This allows one to
- # include the dependency headers using include_directories (SYSTEM ...),
- # such that warnings from these headers do not appear in the nightly builds.
- #
---- seqan2.orig/util/py_lib/pyratemp.py
-+++ seqan2/util/py_lib/pyratemp.py
-@@ -865,7 +865,7 @@
+--- a/util/py_lib/pyratemp.py
++++ b/util/py_lib/pyratemp.py
+@@ -865,7 +865,7 @@ class EvalPseudoSandbox:
Since "import" is insecure, the PseudoSandbox does not allow to
import other modules. But since some functions need to import
other modules (e.g. "datetime.datetime.strftime" imports "time"),
@@ -605,9 +456,9 @@ Description: Fix some spelling issues
modules which are already accessible by the sandboxed code.
:Note:
---- seqan2.orig/apps/fiona/error_rate_from_sam.cpp
-+++ seqan2/apps/fiona/error_rate_from_sam.cpp
-@@ -71,7 +71,7 @@
+--- 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)
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.
@@ -616,9 +467,9 @@ Description: Fix some spelling issues
// Read records
---- seqan2.orig/apps/gustaf/msplazer_main.h
-+++ seqan2/apps/gustaf/msplazer_main.h
-@@ -194,7 +194,7 @@
+--- a/apps/gustaf/msplazer_main.h
++++ b/apps/gustaf/msplazer_main.h
+@@ -194,7 +194,7 @@ int msplazer(StellarOptions & stellarOpt
++sizeCount[length(stellarMatches[i].matches)];
}
for(unsigned i = 0; i < length(sizeCount); ++ i){
@@ -627,9 +478,9 @@ Description: Fix some spelling issues
}
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 @@
+--- a/apps/seqcons2/seqcons_options.cpp
++++ b/apps/seqcons2/seqcons_options.cpp
+@@ -122,7 +122,7 @@ void SeqConsOptions::print(std::ostream
<< "OVERLAP WINDOW SIZE \t" << overlapWindowSize << "\n"
<< "\n"
<< "K-MER SIZE \t" << kMerSize << "\n"
@@ -638,7 +489,7 @@ Description: Fix some spelling issues
<< "\n"
<< "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n"
<< "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n";
-@@ -208,7 +208,7 @@
+@@ -208,7 +208,7 @@ parseCommandLine(SeqConsOptions & option
setMinValue(parser, "k-mer-size", "5");
setDefaultValue(parser, "k-mer-size", "20");
@@ -647,9 +498,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/seqcons_options.h
++++ b/apps/seqcons2/seqcons_options.h
+@@ -100,7 +100,7 @@ struct SeqConsOptions
// K-mer length to use for identifying overlap candidates.
int kMerSize;
@@ -658,9 +509,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -669,9 +520,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -680,9 +531,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/alns1.nop.sam.stderr
++++ b/apps/seqcons2/tests/alns1.nop.sam.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -691,9 +542,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/alns1.nop.txt.stderr
++++ b/apps/seqcons2/tests/alns1.nop.txt.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -702,9 +553,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -713,9 +564,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -724,9 +575,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -735,9 +586,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -746,9 +597,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/alns1.realign.sam.stderr
++++ b/apps/seqcons2/tests/alns1.realign.sam.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -757,9 +608,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/alns1.realign.txt.stderr
++++ b/apps/seqcons2/tests/alns1.realign.txt.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -768,9 +619,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/seqs1.align_consensus.stderr
++++ b/apps/seqcons2/tests/seqs1.align_consensus.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -779,9 +630,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/seqs1.nop.stderr
++++ b/apps/seqcons2/tests/seqs1.nop.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -790,9 +641,9 @@ Description: Fix some spelling issues
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 @@
+--- a/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
++++ b/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
+@@ -16,7 +16,7 @@ OVERLAP MIN COUNT 3
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -801,9 +652,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -812,9 +663,9 @@ Description: Fix some spelling issues
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 @@
+--- 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
OVERLAP WINDOW SIZE 20
K-MER SIZE 20
@@ -823,9 +674,9 @@ Description: Fix some spelling issues
REALIGNMENT BANDWIDTH 10
REALIGNMENT ENVIRONMENT 20
---- seqan2.orig/apps/stellar/README
-+++ seqan2/apps/stellar/README
-@@ -182,7 +182,7 @@
+--- a/apps/stellar/README
++++ b/apps/stellar/README
+@@ -182,7 +182,7 @@ the command line:
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
@@ -834,9 +685,9 @@ 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).
---- seqan2.orig/demos/tutorial/basics/strings.cpp
-+++ seqan2/demos/tutorial/basics/strings.cpp
-@@ -22,7 +22,7 @@
+--- a/demos/tutorial/basics/strings.cpp
++++ b/demos/tutorial/basics/strings.cpp
+@@ -22,7 +22,7 @@ int main()
}
std::cout << std::endl;
//![iterate-and-replace]
@@ -845,7 +696,7 @@ Description: Fix some spelling issues
typedef Size<TAminoAcidString>::Type TSize;
typedef String<TSize> TCounterString;
TCounterString counter;
-@@ -30,7 +30,7 @@
+@@ -30,7 +30,7 @@ int main()
resize(counter, alphSize, 0);
for (TIter it = begin(sourceSeq); it != itEnd; goNext(it))
value(counter, ordValue(value(it))) += 1;
@@ -854,8 +705,8 @@ Description: Fix some spelling issues
//![frequency-table]
typedef Iterator<TCounterString>::Type TCounterIter;
TCounterIter countIt = begin(counter);
---- seqan2.orig/dox/pages/suffix_array.dox
-+++ seqan2/dox/pages/suffix_array.dox
+--- a/dox/pages/suffix_array.dox
++++ b/dox/pages/suffix_array.dox
@@ -13,7 +13,7 @@
* "Faster Suffix Sorting", 1999), and a quicksort based algorithm.
*
@@ -865,9 +716,9 @@ 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).
*
---- seqan2.orig/include/seqan/find/find_base.h
-+++ seqan2/include/seqan/find/find_base.h
-@@ -187,9 +187,9 @@
+--- a/include/seqan/find/find_base.h
++++ b/include/seqan/find/find_base.h
+@@ -187,9 +187,9 @@ struct Needle<Segment<THost, TSpec> cons
* @param[in] k Desired minimal score (for approximate matching). <tt>k</tt> is a number <tt><= 0</tt>.
* Differences are deletions, insertions, and substitutions.
*
@@ -879,9 +730,9 @@ Description: Fix some spelling issues
*
* @section Examples
*
---- seqan2.orig/include/seqan/find/find_begin.h
-+++ seqan2/include/seqan/find/find_begin.h
-@@ -344,7 +344,7 @@
+--- a/include/seqan/find/find_begin.h
++++ b/include/seqan/find/find_begin.h
+@@ -344,7 +344,7 @@ _findBeginInit(TPattern & pattern, TNeed
* @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
@@ -890,9 +741,9 @@ Description: Fix some spelling issues
*
* @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 @@
+--- a/include/seqan/index/index_esa_algs_multi.h
++++ b/include/seqan/index/index_esa_algs_multi.h
+@@ -486,7 +486,7 @@ namespace seqan
template <typename TSTree>
@@ -901,7 +752,7 @@ Description: Fix some spelling issues
public:
typedef typename Value<TSTree>::Type TValue;
-@@ -687,21 +687,21 @@
+@@ -687,21 +687,21 @@ namespace seqan
template < typename TRepeat >
@@ -929,7 +780,7 @@ 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 @@
+@@ -715,23 +715,23 @@ namespace seqan
}
template < typename TRepeat >
@@ -957,8 +808,8 @@ Description: Fix some spelling issues
typedef typename Size<TSTree>::Type Type;
};
---- seqan2.orig/include/seqan/index/index_fm_dox.h
-+++ seqan2/include/seqan/index/index_fm_dox.h
+--- a/include/seqan/index/index_fm_dox.h
++++ b/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).
@@ -968,9 +819,9 @@ Description: Fix some spelling issues
*/
/*!
---- seqan2.orig/include/seqan/statistics/statistics_base.h
-+++ seqan2/include/seqan/statistics/statistics_base.h
-@@ -83,13 +83,13 @@
+--- a/include/seqan/statistics/statistics_base.h
++++ b/include/seqan/statistics/statistics_base.h
+@@ -83,13 +83,13 @@ TFloat _zscore(TStringSet W, TStringSet
}
/*
@@ -988,20 +839,9 @@ 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.
---- seqan2.orig/manual/source/Tutorial/ParsingCommandLineArguments.rst
-+++ seqan2/manual/source/Tutorial/ParsingCommandLineArguments.rst
-@@ -143,7 +143,7 @@
-
- # program -a 1 -a 2 -a 3
-
--If the option ``a`` is not a list then the occurence ``-a 3`` overwrites all previous settings.
-+If the option ``a`` is not a list then the occurrence ``-a 3`` overwrites all previous settings.
-
- However, if ``a`` is marked to be a list, then all values (``1``, ``2``, and ``3``) are stored as its values.
- We can get the number of elements using the function :dox:`ArgumentParser#getOptionValueCount` and then access the individual arguments using the function :dox:`ArgumentParser#getOptionValue`.
---- seqan2.orig/util/py_lib/seqan/dox/proc_doc.py
-+++ seqan2/util/py_lib/seqan/dox/proc_doc.py
-@@ -61,7 +61,7 @@
+--- a/util/py_lib/seqan/dox/proc_doc.py
++++ b/util/py_lib/seqan/dox/proc_doc.py
+@@ -61,7 +61,7 @@ class ProcDoc(object):
"""Collection of the top-level documentation entries.
@ivar doc_processor The DocProcessor that created this ProcDoc.
@@ -1010,9 +850,9 @@ Description: Fix some spelling issues
shortening @link display to second level entries.
"""
---- seqan2.orig/apps/sgip/sgip.cpp
-+++ seqan2/apps/sgip/sgip.cpp
-@@ -72,7 +72,7 @@
+--- a/apps/sgip/sgip.cpp
++++ b/apps/sgip/sgip.cpp
+@@ -72,7 +72,7 @@ enum SearchingType
struct SgipOption
{
// I/O options.
@@ -1021,7 +861,7 @@ 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 @@
+@@ -82,7 +82,7 @@ struct SgipOption
FileOption activeFile;
SearchingType searchingType;
CharString algorithm; // Search strategy for metric dimension,e.g. Greedy, genetic etc.
@@ -1030,7 +870,7 @@ Description: Fix some spelling issues
unsigned cdimension; // metric dimension of comparitive graph specified by user
bool showHelp;
bool showVersion;
-@@ -127,7 +127,7 @@
+@@ -127,7 +127,7 @@ int _sgip(TOption & options)
char const * file1, * file2;
if (!options.isoCheck)
{
@@ -1039,7 +879,7 @@ Description: Fix some spelling issues
if (!_createGraph(g1, SivaLab(), file1))
return 1;
-@@ -137,7 +137,7 @@
+@@ -137,7 +137,7 @@ int _sgip(TOption & options)
}
else
{
@@ -1048,7 +888,7 @@ Description: Fix some spelling issues
file2 = toCString(options.comparFile);
if (!_createGraph(g1, SivaLab(), file1))
return 1;
-@@ -169,9 +169,9 @@
+@@ -169,9 +169,9 @@ void _setupParser(TParser & parser)
{
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
@@ -1060,7 +900,7 @@ 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 @@
+@@ -180,7 +180,7 @@ void _setupParser(TParser & parser)
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"));
@@ -1069,7 +909,7 @@ Description: Fix some spelling issues
setDefaultValue(parser, "odimension", "3");
addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial dimension of comparitive graph by user", ArgParseArgument::INTEGER));
setDefaultValue(parser, "cdimension", "3");
-@@ -212,7 +212,7 @@
+@@ -212,7 +212,7 @@ ArgumentParser::ParseResult _parseOption
return res;
// Extract option value.
--
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