[med-svn] [Git][med-team/abyss][upstream] New upstream version 2.3.5+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat May 14 13:21:32 BST 2022
Étienne Mollier pushed to branch upstream at Debian Med / abyss
Commits:
aa19cce6 by Étienne Mollier at 2022-05-14T13:58:48+02:00
New upstream version 2.3.5+dfsg
- - - - -
15 changed files:
- BloomDBG/bloom-dbg.h
- ChangeLog
- Common/Functional.h
- FilterGraph/FilterGraph.cc
- Graph/ContigGraphAlgorithms.h
- Graph/ExtendPath.h
- Konnector/konnector.cc
- Misc/samtobreak.hs
- PathOverlap/PathOverlap.cpp
- SimpleGraph/SimpleGraph.cpp
- bin/abyss-pe
- configure.ac
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1
Changes:
=====================================
BloomDBG/bloom-dbg.h
=====================================
@@ -175,6 +175,7 @@ seedTypeStr(const SeedType& type)
break;
}
assert(false);
+ return "";
}
/**
@@ -288,6 +289,7 @@ readResultStr(const ReadResult& result)
break;
}
assert(false);
+ return "";
}
/**
@@ -460,7 +462,7 @@ printContig(
unsigned k,
std::ostream& out)
{
- assert(seq.length() >= k);
+ assert(seq.length() >= k); (void)k;
FastaRecord contig;
=====================================
ChangeLog
=====================================
@@ -1,3 +1,12 @@
+2022-05-11 Vladimir Nikolic <vnikolic at bcgsc.ca>
+
+ * Release version 2.3.5
+
+ General:
+ * Fixed compile errors when using the -DNDEBUG flag.
+ * Removed deprecated C++ features.
+
+
2021-12-20 Vladimir Nikolic <vnikolic at bcgsc.ca>
* Release version 2.3.4
=====================================
Common/Functional.h
=====================================
@@ -5,16 +5,22 @@
/** A functor that always returns true. */
template <typename Arg>
-struct True : std::unary_function<Arg, bool> {
+struct True {
bool operator()(const Arg&) const { return true; }
+
+ typedef Arg argument_type;
+ typedef bool result_type;
};
/** A functor to adapt a pointer to a member variable. */
template <typename Arg, typename Result>
-struct MemVar : std::unary_function<Arg, Result>
+struct MemVar
{
MemVar(Result Arg::* p) : m_p(p) { }
Result operator()(const Arg& arg) const { return arg.*m_p; }
+
+ typedef Arg argument_type;
+ typedef Result result_type;
private:
Result Arg::* m_p;
};
@@ -28,8 +34,7 @@ MemVar<Arg, Result> mem_var(Result Arg::* p)
/** A functor, f1(f2(x)). */
template <typename F1, typename F2>
-struct unary_compose : std::unary_function <
- typename F2::argument_type, typename F1::result_type>
+struct unary_compose
{
unary_compose(const F1& f1, const F2& f2) : f1(f1), f2(f2) { }
typename F1::result_type operator()(
@@ -37,6 +42,9 @@ struct unary_compose : std::unary_function <
{
return f1(f2(x));
}
+
+ typedef typename F2::argument_type argument_type;
+ typedef typename F1::result_type result_type;
private:
F1 f1;
F2 f2;
@@ -51,8 +59,7 @@ unary_compose<F1, F2> compose1(const F1& f1, const F2& f2)
/** A functor, f(g1(x), g2(x)). */
template <typename F, typename G1, typename G2>
-struct binary_compose : std::unary_function <
- typename G1::argument_type, typename F::result_type>
+struct binary_compose
{
binary_compose(const F& f, const G1& g1, const G2& g2)
: f(f), g1(g1), g2(g2) { }
@@ -61,6 +68,9 @@ struct binary_compose : std::unary_function <
{
return f(g1(x), g2(x));
}
+
+ typedef typename G1::argument_type argument_type;
+ typedef typename G1::result_type result_type;
private:
F f;
G1 g1;
=====================================
FilterGraph/FilterGraph.cc
=====================================
@@ -382,7 +382,7 @@ removeContigs(Graph& g, vector<vertex_descriptor>& sc)
}
/** Return the value of the bit at the specified index. */
-struct Marked : unary_function<vertex_descriptor, bool>
+struct Marked
{
typedef vector<bool> Data;
Marked(const Graph& g, const Data& data)
@@ -391,6 +391,9 @@ struct Marked : unary_function<vertex_descriptor, bool>
{}
bool operator()(vertex_descriptor u) const { return m_data[get(vertex_contig_index, m_g, u)]; }
+ typedef vertex_descriptor argument_type;
+ typedef bool result_type;
+
private:
const Graph& m_g;
const Data& m_data;
@@ -434,7 +437,7 @@ struct sortContigs
}
};
-struct ShorterThanX : unary_function<vertex_descriptor, bool>
+struct ShorterThanX
{
const Graph& g;
const vector<bool>& seen;
@@ -451,9 +454,12 @@ struct ShorterThanX : unary_function<vertex_descriptor, bool>
return g[y].length < x && !get(vertex_removed, g, y) &&
!seen[get(vertex_contig_index, g, y)];
}
+
+ typedef vertex_descriptor argument_type;
+ typedef bool result_type;
};
-struct LongerThanX : unary_function<vertex_descriptor, bool>
+struct LongerThanX
{
const Graph& g;
const vector<bool>& seen;
@@ -470,9 +476,12 @@ struct LongerThanX : unary_function<vertex_descriptor, bool>
return g[y].length > x && !get(vertex_removed, g, y) &&
!seen[get(vertex_contig_index, g, y)];
}
+
+ typedef vertex_descriptor argument_type;
+ typedef bool result_type;
};
-struct CoverageLessThan : unary_function<vertex_descriptor, bool>
+struct CoverageLessThan
{
const Graph& g;
const vector<bool>& seen;
@@ -491,6 +500,9 @@ struct CoverageLessThan : unary_function<vertex_descriptor, bool>
return meanCoverage < minCov && !get(vertex_removed, g, u) &&
!seen[get(vertex_contig_index, g, u)];
}
+
+ typedef vertex_descriptor argument_type;
+ typedef bool result_type;
};
static void
@@ -549,7 +561,7 @@ getSequence(const Graph& g, vertex_descriptor u)
}
/** Return whether the specified edge is inconsistent. */
-struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
+struct is_edge_inconsistent
{
const Graph& g;
@@ -574,6 +586,9 @@ struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
return true;
return false;
}
+
+ typedef edge_descriptor argument_type;
+ typedef bool result_type;
};
template<typename It>
=====================================
Graph/ContigGraphAlgorithms.h
=====================================
@@ -18,7 +18,7 @@ using boost::graph_traits;
/** Return true if the edge e is a palindrome. */
template<typename Graph>
-struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPalindrome
{
IsPalindrome(const Graph& g)
: m_g(g)
@@ -28,6 +28,9 @@ struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_des
return source(e, m_g) == get(vertex_complement, m_g, target(e, m_g));
}
+ typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+ typedef bool result_type;
+
private:
const Graph& m_g;
};
@@ -223,7 +226,7 @@ assemble(Graph& g, OutIt out)
/** Return true if the edge e is +ve sense. */
template<typename Graph>
-struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPositive
{
IsPositive(const Graph& g)
: m_g(g)
@@ -233,6 +236,9 @@ struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descr
return !get(vertex_sense, m_g, source(e, m_g)) && !get(vertex_sense, m_g, target(e, m_g));
}
+ typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+ typedef bool result_type;
+
private:
const Graph& m_g;
};
@@ -284,7 +290,7 @@ pruneTips_if(Graph& g, OutputIt result, Pred p)
/** Return true if the vertex is a normal 1-in 0-out tip. */
template<typename Graph>
-struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descriptor, bool>
+struct IsTip
{
IsTip(const Graph& g)
: m_g(g)
@@ -294,6 +300,9 @@ struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descript
return in_degree(v, m_g) == 1;
}
+ typedef typename graph_traits<Graph>::vertex_descriptor argument_type;
+ typedef bool result_type;
+
private:
const Graph& m_g;
};
=====================================
Graph/ExtendPath.h
=====================================
@@ -76,6 +76,7 @@ static inline const char* pathExtensionResultStr(PathExtensionResultCode result)
default:
assert(false);
}
+ return "";
}
/** length of path extension (in vertices) and reason for stopping */
=====================================
Konnector/konnector.cc
=====================================
@@ -457,7 +457,7 @@ static inline string calcQual(const FastqRecord& orig,
unsigned extendedRight)
{
assert(extended.length() == orig.seq.length() +
- extendedLeft + extendedRight);
+ extendedLeft + extendedRight); (void)extendedRight;
unsigned char correctedQual = opt::qualityOffset + opt::correctedQual;
string qual(extended.length(), correctedQual);
=====================================
Misc/samtobreak.hs
=====================================
@@ -279,7 +279,7 @@ parseArgs = do
where
help = putStr (usageInfo usage options) >> exitSuccess
tryHelp = "Try 'abyss-samtobreak --help' for more information."
- version = "abyss-samtobreak (ABySS) 2.3.4\n"
+ version = "abyss-samtobreak (ABySS) 2.3.5\n"
usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
\Calculate contig and scaffold contiguity and correctness metrics.\n"
=====================================
PathOverlap/PathOverlap.cpp
=====================================
@@ -507,7 +507,7 @@ mergePaths(const Paths& paths, const OverlapMap& overlaps, const ContigPath& mer
}
/** Return true if the edge e is a path overlap. */
-struct IsPathOverlap : unary_function<edge_descriptor, bool>
+struct IsPathOverlap
{
IsPathOverlap(const Graph& g, const OverlapMap& pmap, const IsPositive<Graph>& pred)
: m_g(g)
@@ -522,6 +522,9 @@ struct IsPathOverlap : unary_function<edge_descriptor, bool>
return stranded && getOverlap(m_pmap, source(e, m_g), target(e, m_g));
}
+ typedef edge_descriptor argument_type;
+ typedef bool result_type;
+
private:
const Graph& m_g;
const OverlapMap& m_pmap;
=====================================
SimpleGraph/SimpleGraph.cpp
=====================================
@@ -305,7 +305,6 @@ static unsigned calculatePathLength(const Graph& g,
/** Compare the lengths of two paths. */
struct ComparePathLength
- : binary_function<ContigPath, ContigPath, bool>
{
ComparePathLength(const Graph& g, const ContigNode& origin)
: m_g(g), m_origin(origin) { }
@@ -315,6 +314,10 @@ struct ComparePathLength
return lenA < lenB
|| (lenA == lenB && a.size() < b.size());
}
+
+ typedef ContigPath first_argument_type;
+ typedef ContigPath second_argument_type;
+ typedef bool result_type;
private:
const Graph& m_g;
const ContigNode& m_origin;
=====================================
bin/abyss-pe
=====================================
@@ -414,7 +414,7 @@ help:
@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
version:
- @echo "abyss-pe (ABySS) 2.3.4"
+ @echo "abyss-pe (ABySS) 2.3.5"
@echo "Written by Shaun Jackman and Anthony Raymond."
@echo
@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.3.4, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.5, abyss-users at bcgsc.ca, abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AC_CONFIG_MACRO_DIR([m4])
=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.4" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands"
.SH NAME
ABYSS \- assemble short reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-pe.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.4" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands"
.SH NAME
abyss-pe - assemble reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-tofastq.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.4" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands"
.SH NAME
abyss-tofastq \- convert various file formats to FASTQ format
.br
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/commit/aa19cce647cacca23ee864dee031abf0b1b479f0
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/commit/aa19cce647cacca23ee864dee031abf0b1b479f0
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