improving bed option

GATB · Mar 1, 2022 · 2dfdfd2 · 2dfdfd2
1 parent bb1f38e
commit 2dfdfd2
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/src/FindBreakpoints.hpp b/src/FindBreakpoints.hpp
@@ -479,8 +479,12 @@ void FindBreakpoints<span>::operator()()
                     v.push_back(token);
                 }
                 if(v[0]==m_chrom_name){ // we are on the current chromosome
-                    interval=std::make_pair(std::stoi(v[1]),std::stoi(v[2]));
-                    interval_vector.push_back( tuple<uint64_t ,uint64_t>(interval));
+                    uint64_t bed_begin = std::stoi(v[1]);
+                    uint64_t bed_end = std::stoi(v[2]);
+                    if ((bed_end-bed_begin) > this->finder->_kmerSize){
+                        interval=std::make_pair(std::stoi(v[1]),std::stoi(v[2]));
+                        interval_vector.push_back( tuple<uint64_t ,uint64_t>(interval));
+                    }
                 }
                 iss.clear();
             }

diff --git a/src/Finder.cpp b/src/Finder.cpp
@@ -431,6 +431,10 @@ void Finder::resumeParameters(){
         getInfo()->add(2,"Graph",getInput()->getStr(STR_URI_GRAPH).c_str());
     }
     getInfo()->add(2,"Reference",getInput()->getStr(STR_URI_REF).c_str());
+    if(getInput()->get(STR_BED) != 0)
+    {
+        getInfo()->add(2,"Bed file",_bed_file_name.c_str());
+    }
     getInfo()->add(1,"Graph");
     getInfo()->add(2,"kmer-size","%i", _kmerSize);