fix mem leak

dellytools · Nov 12, 2020 · 75a0a3f · 75a0a3f
1 parent c0f3900
commit 75a0a3f
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Showing 4 changed files with 29 additions and 26 deletions.
diff --git a/src/annotate.h b/src/annotate.h
@@ -69,14 +69,7 @@ namespace sansa
     }
 
     // Fix chr names
-    fixChrNames(c.nchr);
-
-    // Debug chr names
-    int32_t maxRID = 0;
-    for(AnnotateConfig::TChrMap::const_iterator itcm = c.nchr.begin(); itcm != c.nchr.end(); ++itcm) {
-      if ((int32_t) (itcm->second + 1) > maxRID) maxRID = itcm->second + 1;
-      //std::cerr << itcm->first << '=' << itcm->second << std::endl;
-    }
+    int32_t maxRID = fixChrNames(c);
 
     // Optionally parse GFF/GTF/BED file
     typedef std::vector<IntervalLabel> TChromosomeRegions;

diff --git a/src/parsedb.h b/src/parsedb.h
@@ -129,6 +129,7 @@ namespace sansa
 	}
       }
     }
+    bcf_destroy(rec);
 
     // Sort SVs
     sort(svs.begin(), svs.end(), SortSVs<SV>());
@@ -139,12 +140,9 @@ namespace sansa
 
     // Close output VCF
     bcf_hdr_destroy(hdr_out);
-    hts_close(ofile);
-
-    // Close file handles
     bcf_hdr_destroy(hdr);
+    hts_close(ofile);
     bcf_close(ifile);
-    bcf_destroy(rec);
 
     return true;
   }

diff --git a/src/query.h b/src/query.h
@@ -75,7 +75,7 @@ namespace sansa
 
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
     std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Query input SVs" << std::endl;
-    
+
     // Load bcf file
     htsFile* ifile = bcf_open(c.infile.string().c_str(), "r");
     if (ifile == NULL) {
@@ -150,7 +150,7 @@ namespace sansa
       if (c.gtfFileFormat != -1) geneAnnotation(c, gRegions, geneIds, refIndex, rec->pos + 1, refIndex2, endsv, featureBp1, featureBp2);
       if (featureBp1.empty()) featureBp1 = "NA";
       if (featureBp2.empty()) featureBp2 = "NA";
-      
+
       // Any breakpoint hit?
       typename TSV::iterator itSV = std::lower_bound(svs.begin(), svs.end(), SV(refIndex, std::max(0, startsv - c.bpwindow), refIndex2, endsv), SortSVs<SV>());
       int32_t bestID = -1;
@@ -202,10 +202,11 @@ namespace sansa
 	}
 	dataOut << id << '\t' << bcf_hdr_id2name(hdr, rec->rid) << '\t' << (rec->pos + 1) << '\t' << chr2Name << '\t' <<  endsv << '\t' << rec->d.id << '\t' << qualval << '\t' << svtval << '\t' << ctval << '\t' << svlength << '\t' << featureBp1 << '\t' << featureBp2 << std::endl;
       }
-      
+
       // Successful parse
       ++parsedSV;
     }
+    bcf_destroy(rec);
 
     // Statistics
     now = boost::posix_time::second_clock::local_time();
@@ -214,10 +215,10 @@ namespace sansa
     // Close file handles
     dataOut.pop();
     dataOut.pop();
+
     bcf_hdr_destroy(hdr);
     bcf_close(ifile);
-    bcf_destroy(rec);
-
+
     return true;
   }
 

diff --git a/src/util.h b/src/util.h
@@ -284,15 +284,25 @@ namespace sansa
   }
 
   template<typename TChrMap>
-  inline void
-  fixChrNames(TChrMap& chrMap) {
-    // Take care of 1 vs. chr1, X vs chrX, ...
-    int32_t maxRID = 1;
-    for(typename TChrMap::iterator itcm = chrMap.begin(); itcm != chrMap.end(); ++itcm) {
-      if (itcm->second > maxRID) maxRID = itcm->second + 1;
+  inline int32_t
+  chrMapSize(TChrMap const& chrMap) {
+    int32_t maxRID = 0;
+    for(typename TChrMap::const_iterator itcm = chrMap.begin(); itcm != chrMap.end(); ++itcm) {
+      if (itcm->second >= maxRID) maxRID = itcm->second + 1;
     }
-    std::vector<std::string> altName(maxRID, "NA");
-    for(typename TChrMap::iterator itcm = chrMap.begin(); itcm != chrMap.end(); ++itcm) {
+    return maxRID;
+  }
+
+
+  template<typename TConfig>
+  inline int32_t
+  fixChrNames(TConfig& c) {
+    typedef typename TConfig::TChrMap TChrMap;
+
+    // Take care of 1 vs. chr1, X vs chrX, ...
+    int32_t maxRID = chrMapSize(c.nchr);
+    std::vector<std::string> altName(maxRID);
+    for(typename TChrMap::const_iterator itcm = c.nchr.begin(); itcm != c.nchr.end(); ++itcm) {
       std::string cn = itcm->first;
       if (cn.size() == 1) {
 	if (cn == "1") altName[itcm->second] = "chr1";
@@ -355,8 +365,9 @@ namespace sansa
 
     // Insert alternative names
     for(uint32_t i = 0; i < altName.size(); ++i) {
-      if (altName[i] != "NA") chrMap.insert(std::make_pair(altName[i], i));
+      if (!altName[i].empty()) c.nchr.insert(std::make_pair(altName[i], i));
     }
+    return maxRID;
   }
 
   // Output directory/file checks