From 2dfdfd2c90d9c7cd6b4d386fac17d1d916b14c17 Mon Sep 17 00:00:00 2001
From: Claire Lemaitre <claire.lemaitre@inria.fr>
Date: Tue, 1 Mar 2022 21:58:37 +0100
Subject: [PATCH] improving bed option

---
 src/FindBreakpoints.hpp | 8 ++++++--
 src/Finder.cpp          | 4 ++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/FindBreakpoints.hpp b/src/FindBreakpoints.hpp
index c875720..0477cd9 100644
--- 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
index 0de5f8e..544faf5 100644
--- 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);