drop deprecated func

gear-genomics · Sep 17, 2024 · a1fc8a9 · a1fc8a9
1 parent 7660565
commit a1fc8a9
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Showing 7 changed files with 12 additions and 20 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -23,6 +23,7 @@ RUN apt-get update && apt-get install -y \
     libhdf5-dev \
     libncurses-dev \
     liblzma-dev \
+    pkg-config \
     zlib1g-dev \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*

diff --git a/Makefile b/Makefile
@@ -14,7 +14,7 @@ bindir ?= $(exec_prefix)/bin
 
 # Flags
 CXX=g++
-CXXFLAGS += -std=c++14 -isystem ${JLIB} -isystem ${EBROOTHTSLIB} -isystem ${SDSL_ROOT}/include -pedantic -W -Wall
+CXXFLAGS += -std=c++17 -isystem ${JLIB} -isystem ${EBROOTHTSLIB} -isystem ${SDSL_ROOT}/include -pedantic -W -Wall
 LDFLAGS += -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -L${SDSL_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -ldl -lpthread
 
 ifeq (${STATIC}, 1)

diff --git a/singularity/tracy.def b/singularity/tracy.def
@@ -17,7 +17,7 @@ Stage: build
 
 # Final image
 BootStrap: library
-From: alpine:3.9
+From: alpine:latest
 Stage: final
 
 %files from build

diff --git a/src/assemble.h b/src/assemble.h
@@ -38,17 +38,13 @@ namespace tracy {
     bool forward;
 
     TraceScore(int32_t const s, int32_t const i, int32_t const n, bool const f) : score(s), idx(i), newidx(n), forward(f) {}
-  };
-
 
-  template<typename TTraceScore>
-  struct SortTraceScore : public std::binary_function<TTraceScore, TTraceScore, bool>
-  {
-    inline bool operator()(TTraceScore const& ts1, TTraceScore const& ts2) {
-      return ((ts1.score > ts2.score) || ((ts1.score == ts2.score) && (ts1.idx < ts2.idx)));
+    bool operator<(const TraceScore& ts2) const {
+      return ((score > ts2.score) || ((score == ts2.score) && (idx < ts2.idx)));
     }
   };
-
+
+
   struct SequenceSegment {
     std::string seq;
     int32_t trimLeft;
@@ -248,7 +244,7 @@ namespace tracy {
       }
 
       // Sort score
-      std::sort(scoreIdx.begin(), scoreIdx.end(), SortTraceScore<TraceScore>());
+      std::sort(scoreIdx.begin(), scoreIdx.end());
 
       // Align iteratively
       if (scoreIdx.size()) {

diff --git a/src/indigo.h b/src/indigo.h
@@ -440,7 +440,7 @@ namespace tracy {
       }
 
       // Sort variants
-      std::sort(var.begin(), var.end(), SortVariant<Variant>());
+      std::sort(var.begin(), var.end());
 
       // VCF output
       vcfOutput(c, bc, var, rs);

diff --git a/src/variants.h b/src/variants.h
@@ -16,16 +16,11 @@ namespace tracy {
     std::string id;
 
     Variant(int32_t const p, int32_t const bc, int32_t const g, std::string const& c, std::string const& r, std::string const& a) : pos(p), basenum(bc), gt(g), chr(c), ref(r), alt(a), id(".") {}
-  };
 
-  template<typename TVar>
-  struct SortVariant : public std::binary_function<TVar, TVar, bool>
-  {
-    inline bool operator()(TVar const& var1, TVar const& var2) {
-      return ((var1.chr < var2.chr) || ((var1.chr == var2.chr) && (var1.pos < var2.pos)) || ((var1.chr == var2.chr) && (var1.pos == var2.pos) && (var1.basenum < var2.basenum)));
+    bool operator<(const Variant& var2) const {
+      return ((chr < var2.chr) || ((chr == var2.chr) && (pos < var2.pos)) || ((chr == var2.chr) && (pos == var2.pos) && (basenum < var2.basenum)));
     }
   };
-
 
   inline bool
   strInclN(std::string const& ref) {

diff --git a/src/version.h b/src/version.h
@@ -5,7 +5,7 @@ namespace tracy
 {
 
 
-  std::string tracyVersionNumber = "0.7.6";
+  std::string tracyVersionNumber = "0.7.8";
 
   inline 
     void printTitle(std::string const& title)