drop deprecated func

dellytools · Sep 20, 2024 · c7ffb2d · c7ffb2d
1 parent d1e7b56
commit c7ffb2d
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Showing 7 changed files with 22 additions and 42 deletions.
diff --git a/Makefile b/Makefile
@@ -12,7 +12,7 @@ bindir ?= $(exec_prefix)/bin
 
 # Flags
 CXX ?= g++
-CXXFLAGS += -std=c++11 -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive
+CXXFLAGS += -std=c++17 -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive
 LDFLAGS += -L${EBROOTHTSLIB} -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
 
 # Flags for static compile

diff --git a/src/annotate.h b/src/annotate.h
@@ -110,10 +110,7 @@ namespace sansa
 	std::cerr << "Error parsing GTF/GFF3/BED file!" << std::endl;
 	return 1;
       }
-      for(int32_t refIndex = 0; refIndex < maxRID; ++refIndex) {
-	// Sort by position
-	std::sort(gRegions[refIndex].begin(), gRegions[refIndex].end(), SortIntervalStart<IntervalLabel>());
-      }
+      for(int32_t refIndex = 0; refIndex < maxRID; ++refIndex) std::sort(gRegions[refIndex].begin(), gRegions[refIndex].end());
     }
 
     // Query SV

diff --git a/src/compvcf.h b/src/compvcf.h
@@ -62,17 +62,12 @@ namespace sansa
 
     CompSVRecord() : match(0), tid(0), svStart(0), svEnd(0), svLen(0), svt(0), qual(0), consBp(0), score(0), bestMatchId(0), gtConc(0), nonrefGtConc(0), id(""), allele("") {}
     CompSVRecord(int32_t const t, int32_t const svS) : match(0), tid(t), svStart(svS), svEnd(0), svLen(0), svt(0), qual(0), consBp(0), score(0), bestMatchId(0), gtConc(0), nonrefGtConc(0), id(""), allele("") {}
-  };
 
-  template<typename TSV>
-  struct SortCompSVRecord : public std::binary_function<TSV, TSV, bool>
-  {
-    inline bool operator()(TSV const& sv1, TSV const& sv2) {
-      return ((sv1.tid<sv2.tid) || ((sv1.tid==sv2.tid) && (sv1.svStart<sv2.svStart)) || ((sv1.tid==sv2.tid) && (sv1.svStart==sv2.svStart) && (sv1.svEnd<sv2.svEnd)));
+    bool operator<(const CompSVRecord& sv2) const {
+      return ((tid<sv2.tid) || ((tid==sv2.tid) && (svStart<sv2.svStart)) || ((tid==sv2.tid) && (svStart==sv2.svStart) && (svEnd<sv2.svEnd)));
     }
   };
-
-
+
   struct CompvcfConfig {
     typedef std::map<std::string, uint32_t> TChrMap;
     bool filterForPass;
@@ -100,7 +95,7 @@ namespace sansa
     std::cerr << '[' << boost::posix_time::to_simple_string(boost::posix_time::second_clock::local_time()) << "] " << "Comparing " << compsv.size() << " SVs with " << basesv.size() << " SVs in the base VCF/BCF file " << std::endl;
     for(uint32_t i = 0; i < basesv.size(); ++i) {
       int32_t earliestStart = std::max(basesv[i].svStart - (c.bpdiff + 1), 0);
-      typename TCompSVType::const_iterator itsv = std::lower_bound(compsv.begin(), compsv.end(), CompSVRecord(basesv[i].tid, earliestStart), SortCompSVRecord<CompSVRecord>());
+      typename TCompSVType::const_iterator itsv = std::lower_bound(compsv.begin(), compsv.end(), CompSVRecord(basesv[i].tid, earliestStart));
       for(uint32_t j = (itsv - compsv.begin()); j < compsv.size(); ++j) {
 	if (basesv[i].tid < compsv[j].tid) break;  // Sorted by tid
 	if (c.checkCT) {
@@ -461,8 +456,8 @@ namespace sansa
     if (!_loadCompSVs(c, c.vcffile.string(), compsv)) return -1;
 
     // Sort SVs
-    sort(basesv.begin(), basesv.end(), SortCompSVRecord<CompSVRecord>());
-    sort(compsv.begin(), compsv.end(), SortCompSVRecord<CompSVRecord>());
+    sort(basesv.begin(), basesv.end());
+    sort(compsv.begin(), compsv.end());
 
     // Recall, precission, GT concordance
     compareSVs(c, basesv, compsv);

diff --git a/src/markdup.h b/src/markdup.h
@@ -55,16 +55,12 @@ namespace sansa
     std::vector<float> vaf;
     std::vector<float> gq;
     std::vector<int32_t> gt;
-  };
 
-  template<typename TSV>
-  struct SortSVEvents : public std::binary_function<TSV, TSV, bool>
-  {
-    inline bool operator()(TSV const& sv1, TSV const& sv2) {
-      return ((sv1.tid<sv2.tid) || ((sv1.tid==sv2.tid) && (sv1.svStart<sv2.svStart)) || ((sv1.tid==sv2.tid) && (sv1.svStart==sv2.svStart) && (sv1.svEnd<sv2.svEnd)));
+    bool operator<(const SVEvent& sv2) const {
+      return ((tid<sv2.tid) || ((tid==sv2.tid) && (svStart<sv2.svStart)) || ((tid==sv2.tid) && (svStart==sv2.svStart) && (svEnd<sv2.svEnd)));
     }
   };
-  
+
 
   struct MarkdupConfig {
     bool filterForPass;
@@ -429,7 +425,7 @@ namespace sansa
     if (!_loadSVEvents(c, allsv)) return -1;
 
     // Sort SVs
-    sort(allsv.begin(), allsv.end(), SortSVEvents<SVEvent>());
+    sort(allsv.begin(), allsv.end());
 
     // Mark duplicates
     _markDuplicates(c, allsv);

diff --git a/src/parsedb.h b/src/parsedb.h
@@ -111,7 +111,7 @@ namespace sansa
     bcf_destroy(rec);
 
     // Sort SVs
-    sort(svs.begin(), svs.end(), SortSVs<SV>());
+    sort(svs.begin(), svs.end());
 
     // Statistics
     now = boost::posix_time::second_clock::local_time();

diff --git a/src/query.h b/src/query.h
@@ -174,7 +174,7 @@ namespace sansa
 	if (featureContained.empty()) featureContained = "NA";
 
 	// Any breakpoint hit?
-	typename TSV::iterator itSV = std::lower_bound(svs.begin(), svs.end(), SV(qsv.chr, std::max(0, qsv.svStart - c.bpwindow), qsv.chr2, qsv.svEnd), SortSVs<SV>());
+	typename TSV::iterator itSV = std::lower_bound(svs.begin(), svs.end(), SV(qsv.chr, std::max(0, qsv.svStart - c.bpwindow), qsv.chr2, qsv.svEnd));
 	int32_t bestID = -1;
 	float bestScore = -1;
 	bool noMatch = true;

diff --git a/src/util.h b/src/util.h
@@ -29,24 +29,20 @@ namespace sansa
 
     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) {}
-  };
 
-
-  template<typename TRecord>
-  struct SortIntervalLabel : public std::binary_function<TRecord, TRecord, bool> {
-    inline bool operator()(TRecord const& s1, TRecord const& s2) const {
-      return s1.lid < s2.lid;
+    bool operator<(const IntervalLabel& s2) const {
+      return start < s2.start;
     }
   };
 
+
   template<typename TRecord>
-  struct SortIntervalStart : public std::binary_function<TRecord, TRecord, bool> {
+  struct SortIntervalLabel {
     inline bool operator()(TRecord const& s1, TRecord const& s2) const {
-      return s1.start < s2.start;
+      return s1.lid < s2.lid;
     }
   };
 
-
   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
@@ -69,17 +65,13 @@ namespace sansa
     SV(int32_t const c1, int32_t const pos1, int32_t const c2, int32_t pos2) : chr(c1), svStart(pos1), chr2(c2), svEnd(pos2), id(-1), qual(0), svt(-1), svlen(-1) {}
 
     SV(int32_t const c1, int32_t const pos1, int32_t const c2, int32_t pos2, int32_t const ival, int32_t const qval, int32_t const svtval, int32_t const svl) : chr(c1), svStart(pos1), chr2(c2), svEnd(pos2), id(ival), qual(qval), svt(svtval), svlen(svl) {}
-  };
 
-
-  template<typename TSV>
-  struct SortSVs : public std::binary_function<TSV, TSV, bool>
-  {
-    inline bool operator()(TSV const& sv1, TSV const& sv2) {
-      return ((sv1.chr<sv2.chr) || ((sv1.chr==sv2.chr) && (sv1.svStart<sv2.svStart)) || ((sv1.chr==sv2.chr) && (sv1.svStart==sv2.svStart) && (sv1.chr2<sv2.chr2)) || ((sv1.chr==sv2.chr) && (sv1.svStart==sv2.svStart) && (sv1.chr2==sv2.chr2) && (sv1.svEnd<sv2.svEnd)) || ((sv1.chr==sv2.chr) && (sv1.svStart==sv2.svStart) && (sv1.chr2==sv2.chr2) && (sv1.svEnd==sv2.svEnd) && (sv1.id < sv2.id)));
+    bool operator<(const SV& sv2) const {
+      return ((chr<sv2.chr) || ((chr==sv2.chr) && (svStart<sv2.svStart)) || ((chr==sv2.chr) && (svStart==sv2.svStart) && (chr2<sv2.chr2)) || ((chr==sv2.chr) && (svStart==sv2.svStart) && (chr2==sv2.chr2) && (svEnd<sv2.svEnd)) || ((chr==sv2.chr) && (svStart==sv2.svStart) && (chr2==sv2.chr2) && (svEnd==sv2.svEnd) && (id < sv2.id)));
     }
   };
 
+
   inline bool
   _translocation(int32_t const svt) {
     return (DELLY_SVT_TRANS <= svt) && (svt < 9);