drop deprecated func

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/*

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)

singularity/dicey.def

@@ -17,7 +17,7 @@ Stage: build
 
 # Final image
 BootStrap: library
-From: alpine:3.9
+From: alpine:latest
 Stage: final
 
 %files from build

src/gtf.h

@@ -36,6 +36,10 @@ namespace dicey {
 
     explicit IntervalLabel(int32_t s) : start(s), end(s+1), strand('*'), lid(-1) {}
     IntervalLabel(int32_t s, int32_t e, char t, int32_t l) : start(s), end(e), strand(t), lid(l) {}
+
+    bool operator<(const IntervalLabel& s2) const {
+      return start < s2.start;
+    }
   };
 
   struct IntervalLabelId {
@@ -47,22 +51,19 @@ namespace dicey {
 
     explicit IntervalLabelId(int32_t s) : start(s), end(s+1), strand('*'), lid(-1), eid(-1) {}
     IntervalLabelId(int32_t s, int32_t e, char t, int32_t l, int32_t i) : start(s), end(e), strand(t), lid(l), eid(i) {}
+
+    bool operator<(const IntervalLabelId& s2) const {
+      return start < s2.start;
+    }
   };
 
   template<typename TRecord>
-  struct SortIntervalLabel : public std::binary_function<TRecord, TRecord, bool> {
+  struct SortIntervalLabel {
     inline bool operator()(TRecord const& s1, TRecord const& s2) const {
       return s1.lid < s2.lid;
     }
   };
 
-  template<typename TRecord>
-  struct SortIntervalStart : public std::binary_function<TRecord, TRecord, bool> {
-    inline bool operator()(TRecord const& s1, TRecord const& s2) const {
-      return s1.start < s2.start;
-    }
-  };
-
   inline void
   _insertInterval(std::vector<IntervalLabel>& cr, int32_t s, int32_t e, char strand, int32_t lid, int32_t) {
     // Uniqueness not necessary because we flatten the interval map

src/hunter.h

@@ -58,12 +58,9 @@ namespace dicey
     std::string queryalign;
 
     DnaHit(int32_t sc, uint32_t const refIndex, uint32_t const s, char const orient, std::string const& ra, std::string const& qa) : score(sc), chr(refIndex), start(s), strand(orient), refalign(ra), queryalign(qa) {}
-  };
 
-  template<typename TRecord>
-  struct SortDnaHit : public std::binary_function<TRecord, TRecord, bool> {
-    inline bool operator()(TRecord const& a, TRecord const& b) const {
-      return ((a.score > b.score) || ((a.score == b.score) && (a.chr < b.chr)) || ((a.score == b.score) && (a.chr == b.chr) && (a.start < b.start)));
+    bool operator<(const DnaHit& b) const {
+      return ((score > b.score) || ((score == b.score) && (chr < b.chr)) || ((score == b.score) && (chr == b.chr) && (start < b.start)));
     }
   };
 
@@ -393,7 +390,7 @@ namespace dicey
     }
 
     // Sort
-    std::sort(ht.begin(), ht.end(), SortDnaHit<DnaHit>());
+    std::sort(ht.begin(), ht.end());
 
     // Output
     jsonDnaHitOut(c, seqname, ht, msg);

src/silica.h

@@ -74,16 +74,13 @@ namespace dicey
     double temp;
     double perfTemp;
     std::string genome;
+
+    bool operator<(const PrimerBind& b) const {
+      return (temp > b.temp);
+    }
+
   };
 
-  template<typename TRecord>
-    struct SortPrimer : public std::binary_function<TRecord, TRecord, bool>
-    {
-      inline bool operator()(TRecord const& a, TRecord const& b) const {
-	return (a.temp > b.temp);
-      }
-    };
-
   struct PcrProduct {
     uint32_t refIndex;
     uint32_t leng;
@@ -94,16 +91,12 @@ namespace dicey
     double forTemp;
     double revTemp;
     double penalty;
+
+    bool operator<(const PcrProduct& b) const {
+      return (penalty < b.penalty);
+    }
   };
 
-  template<typename TRecord>
-    struct SortProducts : public std::binary_function<TRecord, TRecord, bool>
-    {
-      inline bool operator()(TRecord const& a, TRecord const& b) const {
-	return (a.penalty < b.penalty);
-      }
-    };
-
   template<typename TConfig, typename TStream>
   inline void
   writeJsonPrimerOut(TConfig const& c, TStream& rcfile, std::vector<std::string> const& qn, std::vector<PrimerBind> const& allp, std::vector<PcrProduct> const& pcrColl, std::vector<std::string> const& pName, std::vector<std::string> const& pSeq, std::vector<std::string> const& msg) {
@@ -588,7 +581,7 @@ namespace dicey
     }
 
     // Sort by temperature
-    std::sort(allp.begin(), allp.end(), SortPrimer<PrimerBind>());
+    std::sort(allp.begin(), allp.end());
 
     // Search PCR amplicons
     if (c.pruneprimer) jsonPrimerOut(c, seqname, allp, pcrColl, pName, pSeq, msg);
@@ -622,7 +615,7 @@ namespace dicey
       }
 
       // Sort by penalty
-      std::sort(pcrColl.begin(), pcrColl.end(), SortProducts<PcrProduct>());
+      std::sort(pcrColl.begin(), pcrColl.end());
 
       // Output amplicons
       jsonPrimerOut(c, seqname, allp, pcrColl, pName, pSeq, msg);

src/version.h

@@ -5,7 +5,7 @@ namespace dicey
 {
 
 
-  std::string diceyVersionNumber = "0.3.1";
+  std::string diceyVersionNumber = "0.3.2";
 
   inline 
   void printTitle(std::string const& title)