Old interval tree

Makefile

@@ -147,7 +147,7 @@ scriptToBin: $(BINS)
 
 GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
 
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
+CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++11 -ggdb
 #CXXFLAGS = -O2
 #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
 

src/Variant.cpp

@@ -314,6 +314,7 @@ bool Variant::canonicalizable(){
 
     if (svtype.empty()){
         // We have no SV type, so we can't interpret things.
+        cerr << "No SV type information. Variant cannot be canonicalized: " << *this << endl;
         return false;
     }
 
@@ -388,10 +389,10 @@ bool Variant::canonicalize(FastaReference& fasta_reference, vector<FastaReferenc
     bool has_end = this->info.count("END") && !this->info.at("END").empty();
 
     // Where is the end, or where should it be?
-    long info_end = 0;
+    int64_t info_end = 0;
     if (has_end) {
         // Get the END from the tag
-        info_end = stol(this->info.at("END")[0]);
+        info_end = stoull(this->info.at("END")[0]);
     }
     else if(ref_valid && !place_seq) {
         // Get the END from the reference sequence, which is ready.
@@ -421,13 +422,13 @@ bool Variant::canonicalize(FastaReference& fasta_reference, vector<FastaReferenc
 
     // What is the variant length change?
     // We store it as absolute value
-    long info_len = 0;
+    int64_t info_len = 0;
     if (has_len){
         // Get the SVLEN from the tag
-        info_len = abs(stol(this->info.at("SVLEN")[0]));
+        info_len = abs(stoll(this->info.at("SVLEN")[0]));
     }
     else if ((svtype == "INS" || svtype == "DEL") && has_span){
-        info_len = abs(stol(this->info.at("SPAN")[0]));
+        info_len = abs(stoll(this->info.at("SPAN")[0]));
     }
     else if (svtype == "DEL"){
         // We always have the end by now
@@ -462,7 +463,7 @@ bool Variant::canonicalize(FastaReference& fasta_reference, vector<FastaReferenc
     has_len = true;
 
     // We also compute a span
-    long info_span = 0;
+    int64_t info_span = 0;
     if (has_span){
         // Use the specified span
         info_span = abs(stol(this->info.at("SVLEN")[0]));

src/vcfnormalizesvs.cpp

@@ -92,7 +92,10 @@ int main(int argc, char** argv) {
 
     Variant var;
     while (variantFile.getNextVariant(var)) {
-        bool valid = var.canonicalize(ref, insertions, replace_sequences, min_size);
+        bool valid = false;
+        if (var.canonicalizable()){
+            valid = var.canonicalize(ref, insertions, replace_sequences, min_size);
+        }
         if (!valid){
             cerr << "Variant could not be normalized" << var << endl;
         }